Downloading Files¶
In [16]:
lwd="/Volumes/Bay3\ scratch/BiGo_manny"
In [17]:
cd {lwd}
/Volumes/Bay3 scratch/BiGo_manny
In []:
#quality trimmed fastq files
!wget http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_HTSdata/BiGo_larvae_cc/BiGo_lar_fastq.tgz
In [3]:
ls
BiGo_lar_fastq.tgz
In [5]:
!tar xvzf BiGo_lar_fastq.tgz
x CgM1_R1a.fastq x CgM1_R2a.fastq x CgM3_R1a.fastq x CgM3_R2a.fastq x CgT1D3_R1a.fastq x CgT1D3_R2a.fastq x CgT1D5_R1a.fastq x CgT1D5_R2a.fastq x CgT3D3_R1a.fastq x CgT3D3_R2a.fastq x CgT3D5_R1a.fastq x CgT3D5_R2a.fastq
In [6]:
#oyster genome
!wget http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa
--2014-07-08 10:20:04-- http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa Resolving eagle.fish.washington.edu... 128.95.149.81 Connecting to eagle.fish.washington.edu|128.95.149.81|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 567608307 (541M) [text/plain] Saving to: `Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa' 100%[======================================>] 567,608,307 10.7M/s in 51s 2014-07-08 10:20:56 (10.5 MB/s) - `Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa' saved [567608307/567608307]
Running BSMAP¶
In [7]:
#setting some variables for files but also
#location of BSMAP (if not in PATH)
bsmaploc="/Volumes/Bay3/Software/BSMAP/bsmap-2.74/"
Another option is running BSMAP on iPlant
In [10]:
lib="CgM1"
In [13]:
! {bsmaploc}bsmap \
-a {lib}_R1a.fastq \
-b {lib}_R2a.fastq \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-o bsmap_out_{lib}.sam \
-p 2
BSMAP v2.74 Start at: Tue Jul 8 10:32:57 2014 Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 13 secs passed total_kmers: 43046721 Create seed table. 56 secs passed max number of mismatches: read_length * 8% max gap size: 0 kmer cut-off ratio: 5e-07 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4 quality cutoff: 0 base quality char: '!' min fragment size:28 max fragemt size:500 start from read #1 end at read #4294967295 additional alignment: T in reads => C in reference mapping strand (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(2 threads) Input read file #1: CgM1_R1a.fastq (format: FASTQ) Input read file #2: CgM1_R2a.fastq (format: FASTQ) Output file: bsmap_out_CgM1.sam (format: SAM) Thread #1: 50000 read pairs finished. 79 secs passed Thread #0: 100000 read pairs finished. 80 secs passed Thread #1: 150000 read pairs finished. 103 secs passed Thread #0: 200000 read pairs finished. 104 secs passed Thread #1: 250000 read pairs finished. 126 secs passed Thread #0: 300000 read pairs finished. 127 secs passed Thread #1: 350000 read pairs finished. 151 secs passed Thread #0: 400000 read pairs finished. 152 secs passed Thread #1: 450000 read pairs finished. 174 secs passed Thread #0: 500000 read pairs finished. 175 secs passed Thread #1: 550000 read pairs finished. 202 secs passed Thread #0: 600000 read pairs finished. 204 secs passed Thread #1: 650000 read pairs finished. 228 secs passed Thread #0: 700000 read pairs finished. 230 secs passed Thread #1: 750000 read pairs finished. 260 secs passed Thread #0: 800000 read pairs finished. 262 secs passed Thread #1: 850000 read pairs finished. 295 secs passed Thread #0: 900000 read pairs finished. 296 secs passed Thread #1: 950000 read pairs finished. 323 secs passed Thread #0: 1000000 read pairs finished. 325 secs passed Thread #1: 1050000 read pairs finished. 407 secs passed Thread #0: 1100000 read pairs finished. 421 secs passed Thread #1: 1150000 read pairs finished. 444 secs passed Thread #0: 1200000 read pairs finished. 444 secs passed Thread #1: 1250000 read pairs finished. 465 secs passed Thread #0: 1300000 read pairs finished. 466 secs passed Thread #1: 1350000 read pairs finished. 486 secs passed Thread #0: 1400000 read pairs finished. 487 secs passed Thread #1: 1450000 read pairs finished. 507 secs passed Thread #0: 1500000 read pairs finished. 508 secs passed Thread #1: 1550000 read pairs finished. 529 secs passed Thread #0: 1600000 read pairs finished. 530 secs passed Thread #1: 1650000 read pairs finished. 550 secs passed Thread #0: 1700000 read pairs finished. 551 secs passed Thread #1: 1750000 read pairs finished. 571 secs passed Thread #0: 1800000 read pairs finished. 572 secs passed Thread #1: 1850000 read pairs finished. 592 secs passed Thread #0: 1900000 read pairs finished. 593 secs passed Thread #1: 1950000 read pairs finished. 613 secs passed Thread #0: 2000000 read pairs finished. 614 secs passed Thread #1: 2050000 read pairs finished. 635 secs passed Thread #0: 2100000 read pairs finished. 635 secs passed Thread #1: 2150000 read pairs finished. 656 secs passed Thread #0: 2200000 read pairs finished. 657 secs passed Thread #1: 2250000 read pairs finished. 678 secs passed Thread #0: 2300000 read pairs finished. 678 secs passed Thread #1: 2350000 read pairs finished. 699 secs passed Thread #0: 2400000 read pairs finished. 700 secs passed Thread #1: 2450000 read pairs finished. 721 secs passed Thread #0: 2500000 read pairs finished. 721 secs passed Thread #1: 2550000 read pairs finished. 744 secs passed Thread #0: 2600000 read pairs finished. 746 secs passed Thread #1: 2650000 read pairs finished. 766 secs passed Thread #0: 2700000 read pairs finished. 767 secs passed Thread #1: 2750000 read pairs finished. 788 secs passed Thread #0: 2800000 read pairs finished. 789 secs passed Thread #1: 2850000 read pairs finished. 810 secs passed Thread #0: 2900000 read pairs finished. 811 secs passed Thread #1: 2950000 read pairs finished. 831 secs passed Thread #0: 3000000 read pairs finished. 832 secs passed Thread #1: 3050000 read pairs finished. 852 secs passed Thread #0: 3100000 read pairs finished. 853 secs passed Thread #1: 3150000 read pairs finished. 873 secs passed Thread #0: 3200000 read pairs finished. 874 secs passed Thread #1: 3250000 read pairs finished. 895 secs passed Thread #0: 3300000 read pairs finished. 895 secs passed Thread #1: 3350000 read pairs finished. 916 secs passed Thread #0: 3400000 read pairs finished. 917 secs passed Thread #1: 3450000 read pairs finished. 937 secs passed Thread #0: 3500000 read pairs finished. 937 secs passed Thread #1: 3550000 read pairs finished. 958 secs passed Thread #0: 3600000 read pairs finished. 958 secs passed Thread #1: 3650000 read pairs finished. 979 secs passed Thread #0: 3700000 read pairs finished. 981 secs passed Thread #1: 3750000 read pairs finished. 1002 secs passed Thread #0: 3800000 read pairs finished. 1003 secs passed Thread #1: 3850000 read pairs finished. 1024 secs passed Thread #0: 3900000 read pairs finished. 1025 secs passed Thread #1: 3950000 read pairs finished. 1045 secs passed Thread #0: 4000000 read pairs finished. 1046 secs passed Thread #1: 4050000 read pairs finished. 1067 secs passed Thread #0: 4100000 read pairs finished. 1068 secs passed Thread #1: 4150000 read pairs finished. 1090 secs passed Thread #0: 4200000 read pairs finished. 1090 secs passed Thread #1: 4250000 read pairs finished. 1112 secs passed Thread #0: 4300000 read pairs finished. 1113 secs passed Thread #1: 4350000 read pairs finished. 1134 secs passed Thread #0: 4400000 read pairs finished. 1135 secs passed Thread #1: 4450000 read pairs finished. 1156 secs passed Thread #0: 4500000 read pairs finished. 1156 secs passed Thread #1: 4550000 read pairs finished. 1177 secs passed Thread #0: 4600000 read pairs finished. 1178 secs passed Thread #1: 4650000 read pairs finished. 1198 secs passed Thread #0: 4700000 read pairs finished. 1199 secs passed Thread #1: 4750000 read pairs finished. 1219 secs passed Thread #0: 4800000 read pairs finished. 1219 secs passed Thread #1: 4850000 read pairs finished. 1240 secs passed Thread #0: 4900000 read pairs finished. 1241 secs passed Thread #1: 4950000 read pairs finished. 1261 secs passed Thread #0: 5000000 read pairs finished. 1262 secs passed Thread #1: 5050000 read pairs finished. 1285 secs passed Thread #0: 5100000 read pairs finished. 1286 secs passed Thread #1: 5150000 read pairs finished. 1312 secs passed Thread #0: 5200000 read pairs finished. 1313 secs passed Thread #1: 5250000 read pairs finished. 1335 secs passed Thread #0: 5300000 read pairs finished. 1335 secs passed Thread #1: 5350000 read pairs finished. 1359 secs passed Thread #0: 5400000 read pairs finished. 1359 secs passed Thread #1: 5450000 read pairs finished. 1380 secs passed Thread #0: 5500000 read pairs finished. 1380 secs passed Thread #1: 5550000 read pairs finished. 1402 secs passed Thread #0: 5600000 read pairs finished. 1402 secs passed Thread #1: 5650000 read pairs finished. 1423 secs passed Thread #0: 5700000 read pairs finished. 1424 secs passed Thread #1: 5750000 read pairs finished. 1446 secs passed Thread #0: 5800000 read pairs finished. 1447 secs passed Thread #1: 5850000 read pairs finished. 1468 secs passed Thread #0: 5900000 read pairs finished. 1469 secs passed Thread #1: 5950000 read pairs finished. 1490 secs passed Thread #0: 6000000 read pairs finished. 1491 secs passed Thread #1: 6050000 read pairs finished. 1511 secs passed Thread #0: 6100000 read pairs finished. 1512 secs passed Thread #1: 6150000 read pairs finished. 1533 secs passed Thread #0: 6200000 read pairs finished. 1534 secs passed Thread #1: 6250000 read pairs finished. 1555 secs passed Thread #0: 6300000 read pairs finished. 1556 secs passed Thread #1: 6350000 read pairs finished. 1576 secs passed Thread #0: 6400000 read pairs finished. 1578 secs passed Thread #1: 6450000 read pairs finished. 1598 secs passed Thread #0: 6500000 read pairs finished. 1599 secs passed Thread #1: 6550000 read pairs finished. 1624 secs passed Thread #0: 6600000 read pairs finished. 1625 secs passed Thread #1: 6650000 read pairs finished. 1645 secs passed Thread #0: 6700000 read pairs finished. 1646 secs passed Thread #1: 6750000 read pairs finished. 1666 secs passed Thread #0: 6800000 read pairs finished. 1667 secs passed Thread #1: 6850000 read pairs finished. 1687 secs passed Thread #0: 6900000 read pairs finished. 1689 secs passed Thread #1: 6950000 read pairs finished. 1709 secs passed Thread #0: 7000000 read pairs finished. 1710 secs passed Thread #1: 7050000 read pairs finished. 1730 secs passed Thread #0: 7100000 read pairs finished. 1731 secs passed Thread #1: 7150000 read pairs finished. 1751 secs passed Thread #0: 7200000 read pairs finished. 1752 secs passed Thread #1: 7250000 read pairs finished. 1773 secs passed Thread #0: 7300000 read pairs finished. 1774 secs passed Thread #1: 7350000 read pairs finished. 1795 secs passed Thread #0: 7400000 read pairs finished. 1795 secs passed Thread #1: 7450000 read pairs finished. 1816 secs passed Thread #0: 7500000 read pairs finished. 1817 secs passed Thread #1: 7550000 read pairs finished. 1837 secs passed Thread #0: 7600000 read pairs finished. 1838 secs passed Thread #1: 7650000 read pairs finished. 1859 secs passed Thread #0: 7700000 read pairs finished. 1859 secs passed Thread #1: 7750000 read pairs finished. 1880 secs passed Thread #0: 7800000 read pairs finished. 1881 secs passed Thread #1: 7850000 read pairs finished. 1901 secs passed Thread #0: 7900000 read pairs finished. 1902 secs passed Thread #1: 7950000 read pairs finished. 1923 secs passed Thread #0: 8000000 read pairs finished. 1924 secs passed Thread #1: 8050000 read pairs finished. 1944 secs passed Thread #0: 8100000 read pairs finished. 1945 secs passed Thread #1: 8150000 read pairs finished. 1965 secs passed Thread #0: 8200000 read pairs finished. 1966 secs passed Thread #0: 8297202 read pairs finished. 1986 secs passed Thread #1: 8250000 read pairs finished. 1987 secs passed Total number of aligned reads: pairs: 3832546 (46%) single a: 1591687 (19%) single b: 1349271 (16%) Done. Finished at Tue Jul 8 11:06:04 2014 Total time consumed: 1987 secs
In [16]:
lib="CgT1D3"
In [17]:
! {bsmaploc}bsmap \
-a {lib}_R1a.fastq \
-b {lib}_R2a.fastq \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-o bsmap_out_{lib}.sam \
-p 2 \
;
BSMAP v2.74 Start at: Tue Jul 8 11:56:33 2014 Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 13 secs passed total_kmers: 43046721 Create seed table. 69 secs passed max number of mismatches: read_length * 8% max gap size: 0 kmer cut-off ratio: 5e-07 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4 quality cutoff: 0 base quality char: '!' min fragment size:28 max fragemt size:500 start from read #1 end at read #4294967295 additional alignment: T in reads => C in reference mapping strand (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(2 threads) Input read file #1: CgT1D3_R1a.fastq (format: FASTQ) Input read file #2: CgT1D3_R2a.fastq (format: FASTQ) Output file: bsmap_out_CgT1D3.sam (format: SAM) Thread #1: 100000 read pairs finished. 104 secs passed Thread #0: 50000 read pairs finished. 106 secs passed Thread #1: 150000 read pairs finished. 139 secs passed Thread #0: 200000 read pairs finished. 139 secs passed Thread #1: 250000 read pairs finished. 160 secs passed Thread #0: 300000 read pairs finished. 161 secs passed Thread #1: 350000 read pairs finished. 182 secs passed Thread #0: 400000 read pairs finished. 182 secs passed Thread #1: 450000 read pairs finished. 203 secs passed Thread #0: 500000 read pairs finished. 203 secs passed Thread #1: 550000 read pairs finished. 226 secs passed Thread #0: 600000 read pairs finished. 229 secs passed Thread #1: 650000 read pairs finished. 252 secs passed Thread #0: 700000 read pairs finished. 256 secs passed Thread #1: 750000 read pairs finished. 276 secs passed Thread #0: 800000 read pairs finished. 278 secs passed Thread #1: 850000 read pairs finished. 301 secs passed Thread #0: 900000 read pairs finished. 302 secs passed Thread #1: 950000 read pairs finished. 323 secs passed Thread #0: 1000000 read pairs finished. 324 secs passed Thread #1: 1050000 read pairs finished. 345 secs passed Thread #0: 1100000 read pairs finished. 346 secs passed Thread #1: 1150000 read pairs finished. 374 secs passed Thread #0: 1200000 read pairs finished. 375 secs passed Thread #1: 1250000 read pairs finished. 407 secs passed Thread #0: 1300000 read pairs finished. 408 secs passed Thread #1: 1350000 read pairs finished. 440 secs passed Thread #0: 1400000 read pairs finished. 440 secs passed Thread #1: 1450000 read pairs finished. 462 secs passed Thread #0: 1500000 read pairs finished. 463 secs passed Thread #1: 1550000 read pairs finished. 487 secs passed Thread #0: 1600000 read pairs finished. 488 secs passed Thread #1: 1650000 read pairs finished. 515 secs passed Thread #0: 1700000 read pairs finished. 516 secs passed Thread #1: 1750000 read pairs finished. 544 secs passed Thread #0: 1800000 read pairs finished. 544 secs passed Thread #1: 1850000 read pairs finished. 578 secs passed Thread #0: 1900000 read pairs finished. 578 secs passed Thread #1: 1950000 read pairs finished. 601 secs passed Thread #0: 2000000 read pairs finished. 602 secs passed Thread #1: 2050000 read pairs finished. 630 secs passed Thread #0: 2100000 read pairs finished. 631 secs passed Thread #1: 2150000 read pairs finished. 658 secs passed Thread #0: 2200000 read pairs finished. 660 secs passed Thread #1: 2250000 read pairs finished. 682 secs passed Thread #0: 2300000 read pairs finished. 684 secs passed Thread #1: 2350000 read pairs finished. 707 secs passed Thread #0: 2400000 read pairs finished. 707 secs passed Thread #1: 2450000 read pairs finished. 731 secs passed Thread #0: 2500000 read pairs finished. 732 secs passed Thread #1: 2550000 read pairs finished. 766 secs passed Thread #0: 2600000 read pairs finished. 767 secs passed Thread #1: 2650000 read pairs finished. 793 secs passed Thread #0: 2700000 read pairs finished. 794 secs passed Thread #1: 2750000 read pairs finished. 818 secs passed Thread #0: 2800000 read pairs finished. 819 secs passed Thread #1: 2850000 read pairs finished. 841 secs passed Thread #0: 2900000 read pairs finished. 842 secs passed Thread #1: 2950000 read pairs finished. 862 secs passed Thread #0: 3000000 read pairs finished. 863 secs passed Thread #1: 3050000 read pairs finished. 887 secs passed Thread #0: 3100000 read pairs finished. 887 secs passed Thread #1: 3150000 read pairs finished. 909 secs passed Thread #0: 3200000 read pairs finished. 910 secs passed Thread #1: 3250000 read pairs finished. 930 secs passed Thread #0: 3300000 read pairs finished. 931 secs passed Thread #1: 3350000 read pairs finished. 952 secs passed Thread #0: 3400000 read pairs finished. 953 secs passed Thread #1: 3450000 read pairs finished. 982 secs passed Thread #0: 3500000 read pairs finished. 986 secs passed Thread #1: 3550000 read pairs finished. 1015 secs passed Thread #0: 3600000 read pairs finished. 1017 secs passed Thread #1: 3650000 read pairs finished. 1041 secs passed Thread #0: 3700000 read pairs finished. 1042 secs passed Thread #1: 3750000 read pairs finished. 1063 secs passed Thread #0: 3800000 read pairs finished. 1065 secs passed Thread #1: 3850000 read pairs finished. 1086 secs passed Thread #0: 3900000 read pairs finished. 1087 secs passed Thread #1: 3950000 read pairs finished. 1108 secs passed Thread #0: 4000000 read pairs finished. 1109 secs passed Thread #1: 4050000 read pairs finished. 1130 secs passed Thread #0: 4100000 read pairs finished. 1131 secs passed Thread #1: 4150000 read pairs finished. 1152 secs passed Thread #0: 4200000 read pairs finished. 1153 secs passed Thread #1: 4250000 read pairs finished. 1174 secs passed Thread #0: 4300000 read pairs finished. 1175 secs passed Thread #1: 4350000 read pairs finished. 1196 secs passed Thread #0: 4400000 read pairs finished. 1197 secs passed Thread #1: 4450000 read pairs finished. 1217 secs passed Thread #0: 4500000 read pairs finished. 1218 secs passed Thread #1: 4550000 read pairs finished. 1239 secs passed Thread #0: 4600000 read pairs finished. 1239 secs passed Thread #1: 4650000 read pairs finished. 1261 secs passed Thread #0: 4700000 read pairs finished. 1261 secs passed Thread #1: 4750000 read pairs finished. 1287 secs passed Thread #0: 4800000 read pairs finished. 1287 secs passed Thread #1: 4850000 read pairs finished. 1315 secs passed Thread #0: 4900000 read pairs finished. 1316 secs passed Thread #1: 4950000 read pairs finished. 1337 secs passed Thread #0: 5000000 read pairs finished. 1339 secs passed Thread #1: 5050000 read pairs finished. 1360 secs passed Thread #0: 5100000 read pairs finished. 1361 secs passed Thread #1: 5150000 read pairs finished. 1382 secs passed Thread #0: 5200000 read pairs finished. 1383 secs passed Thread #1: 5250000 read pairs finished. 1405 secs passed Thread #0: 5300000 read pairs finished. 1405 secs passed Thread #1: 5350000 read pairs finished. 1426 secs passed Thread #0: 5400000 read pairs finished. 1427 secs passed Thread #0: 5465974 read pairs finished. 1434 secs passed Thread #1: 5450000 read pairs finished. 1448 secs passed Total number of aligned reads: pairs: 2625402 (48%) single a: 1124227 (21%) single b: 885757 (16%) Done. Finished at Tue Jul 8 12:20:41 2014 Total time consumed: 1448 secs
In [19]:
lib="CgT1D5"
In [20]:
! {bsmaploc}bsmap \
-a {lib}_R1a.fastq \
-b {lib}_R2a.fastq \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-o bsmap_out_{lib}.sam \
-p 4 ; \
BSMAP v2.74 Start at: Tue Jul 8 12:26:49 2014 Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 13 secs passed total_kmers: 43046721 Create seed table. 56 secs passed max number of mismatches: read_length * 8% max gap size: 0 kmer cut-off ratio: 5e-07 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4 quality cutoff: 0 base quality char: '!' min fragment size:28 max fragemt size:500 start from read #1 end at read #4294967295 additional alignment: T in reads => C in reference mapping strand (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(4 threads) Input read file #1: CgT1D5_R1a.fastq (format: FASTQ) Input read file #2: CgT1D5_R2a.fastq (format: FASTQ) Output file: bsmap_out_CgT1D5.sam (format: SAM) Thread #3: 150000 read pairs finished. 105 secs passed Thread #0: 100000 read pairs finished. 106 secs passed Thread #2: 200000 read pairs finished. 106 secs passed Thread #1: 50000 read pairs finished. 107 secs passed Thread #3: 250000 read pairs finished. 150 secs passed Thread #0: 300000 read pairs finished. 151 secs passed Thread #2: 350000 read pairs finished. 152 secs passed Thread #1: 400000 read pairs finished. 152 secs passed Thread #3: 450000 read pairs finished. 203 secs passed Thread #1: 600000 read pairs finished. 206 secs passed Thread #2: 550000 read pairs finished. 207 secs passed Thread #0: 500000 read pairs finished. 210 secs passed Thread #3: 650000 read pairs finished. 245 secs passed Thread #1: 700000 read pairs finished. 250 secs passed Thread #2: 750000 read pairs finished. 250 secs passed Thread #0: 800000 read pairs finished. 253 secs passed Thread #3: 850000 read pairs finished. 284 secs passed Thread #1: 900000 read pairs finished. 288 secs passed Thread #2: 950000 read pairs finished. 289 secs passed Thread #0: 1000000 read pairs finished. 290 secs passed Thread #3: 1050000 read pairs finished. 323 secs passed Thread #1: 1100000 read pairs finished. 328 secs passed Thread #2: 1150000 read pairs finished. 328 secs passed Thread #0: 1200000 read pairs finished. 331 secs passed Thread #3: 1250000 read pairs finished. 362 secs passed Thread #1: 1300000 read pairs finished. 365 secs passed Thread #2: 1350000 read pairs finished. 368 secs passed Thread #0: 1400000 read pairs finished. 369 secs passed Thread #3: 1450000 read pairs finished. 400 secs passed Thread #1: 1500000 read pairs finished. 402 secs passed Thread #2: 1550000 read pairs finished. 405 secs passed Thread #0: 1600000 read pairs finished. 407 secs passed Thread #3: 1650000 read pairs finished. 454 secs passed Thread #1: 1700000 read pairs finished. 457 secs passed Thread #2: 1750000 read pairs finished. 460 secs passed Thread #0: 1800000 read pairs finished. 463 secs passed Thread #1: 1900000 read pairs finished. 502 secs passed Thread #3: 1850000 read pairs finished. 503 secs passed Thread #2: 1950000 read pairs finished. 503 secs passed Thread #0: 2000000 read pairs finished. 505 secs passed Thread #1: 2050000 read pairs finished. 544 secs passed Thread #3: 2100000 read pairs finished. 545 secs passed Thread #2: 2150000 read pairs finished. 545 secs passed Thread #0: 2200000 read pairs finished. 545 secs passed Thread #1: 2250000 read pairs finished. 587 secs passed Thread #3: 2300000 read pairs finished. 588 secs passed Thread #2: 2350000 read pairs finished. 589 secs passed Thread #0: 2400000 read pairs finished. 590 secs passed Thread #1: 2450000 read pairs finished. 627 secs passed Thread #3: 2500000 read pairs finished. 628 secs passed Thread #2: 2550000 read pairs finished. 630 secs passed Thread #0: 2600000 read pairs finished. 631 secs passed Thread #1: 2650000 read pairs finished. 675 secs passed Thread #3: 2700000 read pairs finished. 678 secs passed Thread #2: 2750000 read pairs finished. 683 secs passed Thread #0: 2800000 read pairs finished. 686 secs passed Thread #1: 2850000 read pairs finished. 734 secs passed Thread #3: 2900000 read pairs finished. 736 secs passed Thread #2: 2950000 read pairs finished. 740 secs passed Thread #0: 3000000 read pairs finished. 741 secs passed Thread #1: 3050000 read pairs finished. 792 secs passed Thread #3: 3100000 read pairs finished. 792 secs passed Thread #2: 3150000 read pairs finished. 797 secs passed Thread #0: 3200000 read pairs finished. 799 secs passed Thread #1: 3250000 read pairs finished. 841 secs passed Thread #3: 3300000 read pairs finished. 842 secs passed Thread #2: 3350000 read pairs finished. 846 secs passed Thread #0: 3400000 read pairs finished. 848 secs passed Thread #3: 3500000 read pairs finished. 891 secs passed Thread #1: 3450000 read pairs finished. 892 secs passed Thread #2: 3550000 read pairs finished. 895 secs passed Thread #0: 3600000 read pairs finished. 897 secs passed Thread #1: 3700000 read pairs finished. 941 secs passed Thread #3: 3650000 read pairs finished. 942 secs passed Thread #2: 3750000 read pairs finished. 945 secs passed Thread #0: 3800000 read pairs finished. 947 secs passed Thread #1: 3850000 read pairs finished. 992 secs passed Thread #3: 3900000 read pairs finished. 992 secs passed Thread #2: 3950000 read pairs finished. 994 secs passed Thread #0: 4000000 read pairs finished. 996 secs passed Thread #1: 4050000 read pairs finished. 1038 secs passed Thread #3: 4100000 read pairs finished. 1039 secs passed Thread #2: 4150000 read pairs finished. 1041 secs passed Thread #0: 4200000 read pairs finished. 1043 secs passed Thread #1: 4250000 read pairs finished. 1085 secs passed Thread #3: 4300000 read pairs finished. 1086 secs passed Thread #2: 4350000 read pairs finished. 1088 secs passed Thread #0: 4400000 read pairs finished. 1091 secs passed Thread #1: 4450000 read pairs finished. 1132 secs passed Thread #3: 4500000 read pairs finished. 1133 secs passed Thread #2: 4550000 read pairs finished. 1134 secs passed Thread #0: 4600000 read pairs finished. 1138 secs passed Thread #1: 4650000 read pairs finished. 1178 secs passed Thread #3: 4700000 read pairs finished. 1180 secs passed Thread #2: 4750000 read pairs finished. 1181 secs passed Thread #0: 4800000 read pairs finished. 1185 secs passed Thread #1: 4850000 read pairs finished. 1241 secs passed Thread #3: 4900000 read pairs finished. 1244 secs passed Thread #2: 4950000 read pairs finished. 1246 secs passed Thread #0: 5000000 read pairs finished. 1255 secs passed Thread #1: 5050000 read pairs finished. 1341 secs passed Thread #3: 5100000 read pairs finished. 1343 secs passed Thread #2: 5150000 read pairs finished. 1343 secs passed Thread #0: 5200000 read pairs finished. 1348 secs passed Thread #1: 5250000 read pairs finished. 1410 secs passed Thread #2: 5350000 read pairs finished. 1415 secs passed Thread #3: 5300000 read pairs finished. 1416 secs passed Thread #0: 5400000 read pairs finished. 1422 secs passed Thread #1: 5450000 read pairs finished. 1541 secs passed Thread #2: 5500000 read pairs finished. 1549 secs passed Thread #3: 5550000 read pairs finished. 1551 secs passed Thread #0: 5600000 read pairs finished. 1559 secs passed Thread #1: 5650000 read pairs finished. 1701 secs passed Thread #2: 5700000 read pairs finished. 1709 secs passed Thread #3: 5750000 read pairs finished. 1711 secs passed Thread #0: 5800000 read pairs finished. 1720 secs passed Thread #1: 5850000 read pairs finished. 1872 secs passed Thread #2: 5900000 read pairs finished. 1881 secs passed Thread #3: 5950000 read pairs finished. 1883 secs passed Thread #0: 6000000 read pairs finished. 1892 secs passed Thread #1: 6050000 read pairs finished. 2016 secs passed Thread #2: 6100000 read pairs finished. 2018 secs passed Thread #3: 6150000 read pairs finished. 2021 secs passed Thread #0: 6200000 read pairs finished. 2025 secs passed Thread #3: 6327160 read pairs finished. 2053 secs passed Thread #1: 6250000 read pairs finished. 2079 secs passed Thread #2: 6300000 read pairs finished. 2081 secs passed Total number of aligned reads: pairs: 2608088 (41%) single a: 1736286 (27%) single b: 1343344 (21%) Done. Finished at Tue Jul 8 13:01:31 2014 Total time consumed: 2082 secs
In [21]:
lib="CgM3"
In [22]:
! {bsmaploc}bsmap \
-a {lib}_R1a.fastq \
-b {lib}_R2a.fastq \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-o bsmap_out_{lib}.sam \
-p 4 \
BSMAP v2.74 Start at: Tue Jul 8 13:01:33 2014 Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 22 secs passed total_kmers: 43046721 Create seed table. 78 secs passed max number of mismatches: read_length * 8% max gap size: 0 kmer cut-off ratio: 5e-07 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4 quality cutoff: 0 base quality char: '!' min fragment size:28 max fragemt size:500 start from read #1 end at read #4294967295 additional alignment: T in reads => C in reference mapping strand (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(4 threads) Input read file #1: CgM3_R1a.fastq (format: FASTQ) Input read file #2: CgM3_R2a.fastq (format: FASTQ) Output file: bsmap_out_CgM3.sam (format: SAM) Thread #2: 200000 read pairs finished. 142 secs passed Thread #0: 150000 read pairs finished. 143 secs passed Thread #1: 100000 read pairs finished. 143 secs passed Thread #3: 50000 read pairs finished. 144 secs passed Thread #2: 250000 read pairs finished. 218 secs passed Thread #0: 300000 read pairs finished. 219 secs passed Thread #1: 350000 read pairs finished. 222 secs passed Thread #3: 400000 read pairs finished. 223 secs passed Thread #2: 450000 read pairs finished. 311 secs passed Thread #0: 500000 read pairs finished. 313 secs passed Thread #1: 550000 read pairs finished. 316 secs passed Thread #3: 600000 read pairs finished. 316 secs passed Thread #2: 650000 read pairs finished. 384 secs passed Thread #0: 700000 read pairs finished. 384 secs passed Thread #3: 800000 read pairs finished. 386 secs passed Thread #1: 750000 read pairs finished. 387 secs passed Thread #2: 850000 read pairs finished. 499 secs passed Thread #0: 900000 read pairs finished. 502 secs passed Thread #3: 950000 read pairs finished. 527 secs passed Thread #1: 1000000 read pairs finished. 536 secs passed Thread #0: 1100000 read pairs finished. 650 secs passed Thread #2: 1050000 read pairs finished. 654 secs passed Thread #3: 1150000 read pairs finished. 667 secs passed Thread #1: 1200000 read pairs finished. 677 secs passed Thread #0: 1250000 read pairs finished. 777 secs passed Thread #2: 1300000 read pairs finished. 779 secs passed Thread #3: 1350000 read pairs finished. 784 secs passed Thread #1: 1400000 read pairs finished. 792 secs passed Thread #0: 1450000 read pairs finished. 874 secs passed Thread #2: 1500000 read pairs finished. 877 secs passed Thread #3: 1550000 read pairs finished. 881 secs passed Thread #1: 1600000 read pairs finished. 891 secs passed Thread #0: 1650000 read pairs finished. 974 secs passed Thread #2: 1700000 read pairs finished. 976 secs passed Thread #3: 1750000 read pairs finished. 980 secs passed Thread #1: 1800000 read pairs finished. 993 secs passed Thread #0: 1850000 read pairs finished. 1072 secs passed Thread #2: 1900000 read pairs finished. 1072 secs passed Thread #3: 1950000 read pairs finished. 1076 secs passed Thread #1: 2000000 read pairs finished. 1091 secs passed Thread #0: 2050000 read pairs finished. 1170 secs passed Thread #2: 2100000 read pairs finished. 1173 secs passed Thread #3: 2150000 read pairs finished. 1177 secs passed Thread #1: 2200000 read pairs finished. 1188 secs passed Thread #0: 2250000 read pairs finished. 1259 secs passed Thread #2: 2300000 read pairs finished. 1260 secs passed Thread #3: 2350000 read pairs finished. 1264 secs passed Thread #1: 2400000 read pairs finished. 1277 secs passed Thread #0: 2450000 read pairs finished. 1342 secs passed Thread #2: 2500000 read pairs finished. 1344 secs passed Thread #3: 2550000 read pairs finished. 1347 secs passed Thread #1: 2600000 read pairs finished. 1360 secs passed Thread #0: 2650000 read pairs finished. 1445 secs passed Thread #2: 2700000 read pairs finished. 1448 secs passed Thread #3: 2750000 read pairs finished. 1455 secs passed Thread #1: 2800000 read pairs finished. 1479 secs passed Thread #0: 2850000 read pairs finished. 1570 secs passed Thread #2: 2900000 read pairs finished. 1571 secs passed Thread #3: 2950000 read pairs finished. 1576 secs passed Thread #1: 3000000 read pairs finished. 1591 secs passed Thread #0: 3050000 read pairs finished. 1655 secs passed Thread #2: 3100000 read pairs finished. 1656 secs passed Thread #3: 3150000 read pairs finished. 1659 secs passed Thread #1: 3200000 read pairs finished. 1676 secs passed Thread #0: 3250000 read pairs finished. 1738 secs passed Thread #2: 3300000 read pairs finished. 1740 secs passed Thread #3: 3350000 read pairs finished. 1744 secs passed Thread #1: 3400000 read pairs finished. 1762 secs passed Thread #0: 3450000 read pairs finished. 1838 secs passed Thread #2: 3500000 read pairs finished. 1841 secs passed Thread #3: 3550000 read pairs finished. 1846 secs passed Thread #1: 3600000 read pairs finished. 1868 secs passed Thread #0: 3650000 read pairs finished. 1959 secs passed Thread #2: 3700000 read pairs finished. 1973 secs passed Thread #3: 3750000 read pairs finished. 1983 secs passed Thread #1: 3800000 read pairs finished. 2001 secs passed Thread #0: 3850000 read pairs finished. 2072 secs passed Thread #2: 3900000 read pairs finished. 2081 secs passed Thread #3: 3950000 read pairs finished. 2088 secs passed Thread #1: 4000000 read pairs finished. 2105 secs passed Thread #0: 4050000 read pairs finished. 2166 secs passed Thread #2: 4100000 read pairs finished. 2178 secs passed Thread #3: 4150000 read pairs finished. 2184 secs passed Thread #1: 4200000 read pairs finished. 2202 secs passed Thread #0: 4250000 read pairs finished. 2268 secs passed Thread #2: 4300000 read pairs finished. 2278 secs passed Thread #3: 4350000 read pairs finished. 2285 secs passed Thread #1: 4400000 read pairs finished. 2304 secs passed Thread #0: 4450000 read pairs finished. 2366 secs passed Thread #2: 4500000 read pairs finished. 2376 secs passed Thread #3: 4550000 read pairs finished. 2382 secs passed Thread #1: 4600000 read pairs finished. 2404 secs passed Thread #0: 4650000 read pairs finished. 2469 secs passed Thread #2: 4700000 read pairs finished. 2477 secs passed Thread #3: 4750000 read pairs finished. 2481 secs passed Thread #1: 4800000 read pairs finished. 2506 secs passed Thread #0: 4850000 read pairs finished. 2587 secs passed Thread #2: 4900000 read pairs finished. 2605 secs passed Thread #3: 4950000 read pairs finished. 2611 secs passed Thread #1: 5000000 read pairs finished. 2635 secs passed Thread #0: 5050000 read pairs finished. 2704 secs passed Thread #2: 5100000 read pairs finished. 2716 secs passed Thread #3: 5150000 read pairs finished. 2721 secs passed Thread #1: 5200000 read pairs finished. 2747 secs passed Thread #0: 5250000 read pairs finished. 2810 secs passed Thread #2: 5300000 read pairs finished. 2824 secs passed Thread #3: 5350000 read pairs finished. 2830 secs passed Thread #1: 5400000 read pairs finished. 2869 secs passed Thread #0: 5450000 read pairs finished. 2956 secs passed Thread #2: 5500000 read pairs finished. 2974 secs passed Thread #3: 5550000 read pairs finished. 2978 secs passed Thread #1: 5600000 read pairs finished. 3023 secs passed Thread #0: 5650000 read pairs finished. 3109 secs passed Thread #2: 5700000 read pairs finished. 3122 secs passed Thread #3: 5750000 read pairs finished. 3124 secs passed Thread #1: 5800000 read pairs finished. 3164 secs passed Thread #0: 5850000 read pairs finished. 3254 secs passed Thread #2: 5900000 read pairs finished. 3269 secs passed Thread #3: 5950000 read pairs finished. 3270 secs passed Thread #1: 6000000 read pairs finished. 3306 secs passed Thread #0: 6050000 read pairs finished. 3391 secs passed Thread #3: 6150000 read pairs finished. 3403 secs passed Thread #2: 6100000 read pairs finished. 3404 secs passed Thread #1: 6200000 read pairs finished. 3439 secs passed Thread #0: 6250000 read pairs finished. 3500 secs passed Thread #3: 6300000 read pairs finished. 3512 secs passed Thread #2: 6350000 read pairs finished. 3514 secs passed Thread #1: 6400000 read pairs finished. 3549 secs passed Thread #0: 6450000 read pairs finished. 3588 secs passed Thread #3: 6500000 read pairs finished. 3594 secs passed Thread #2: 6550000 read pairs finished. 3596 secs passed Thread #1: 6600000 read pairs finished. 3613 secs passed Thread #0: 6650000 read pairs finished. 3667 secs passed Thread #3: 6700000 read pairs finished. 3672 secs passed Thread #2: 6750000 read pairs finished. 3674 secs passed Thread #1: 6800000 read pairs finished. 3712 secs passed Thread #0: 6850000 read pairs finished. 3749 secs passed Thread #3: 6900000 read pairs finished. 3761 secs passed Thread #2: 6950000 read pairs finished. 3766 secs passed Thread #1: 7000000 read pairs finished. 3824 secs passed Thread #0: 7050000 read pairs finished. 3907 secs passed Thread #3: 7100000 read pairs finished. 3916 secs passed Thread #2: 7150000 read pairs finished. 3924 secs passed Thread #1: 7200000 read pairs finished. 3976 secs passed Thread #0: 7250000 read pairs finished. 4060 secs passed Thread #3: 7300000 read pairs finished. 4068 secs passed Thread #2: 7350000 read pairs finished. 4073 secs passed Thread #1: 7400000 read pairs finished. 4140 secs passed Thread #0: 7450000 read pairs finished. 4238 secs passed Thread #3: 7500000 read pairs finished. 4247 secs passed Thread #2: 7550000 read pairs finished. 4252 secs passed Thread #1: 7600000 read pairs finished. 4308 secs passed Thread #0: 7650000 read pairs finished. 4369 secs passed Thread #3: 7700000 read pairs finished. 4379 secs passed Thread #2: 7750000 read pairs finished. 4384 secs passed Thread #1: 7800000 read pairs finished. 4429 secs passed Thread #0: 7850000 read pairs finished. 4500 secs passed Thread #3: 7900000 read pairs finished. 4513 secs passed Thread #2: 7950000 read pairs finished. 4521 secs passed Thread #1: 8000000 read pairs finished. 4554 secs passed Thread #3: 8078115 read pairs finished. 4564 secs passed Thread #0: 8050000 read pairs finished. 4580 secs passed Total number of aligned reads: pairs: 4380128 (54%) single a: 1426879 (18%) single b: 1168161 (14%) Done. Finished at Tue Jul 8 14:17:54 2014 Total time consumed: 4581 secs
In [23]:
lib="CgT3D3"
In [24]:
! {bsmaploc}bsmap \
-a {lib}_R1a.fastq \
-b {lib}_R2a.fastq \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-o bsmap_out_{lib}.sam \
-p 4 \
BSMAP v2.74 Start at: Tue Jul 8 14:17:56 2014 Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 21 secs passed total_kmers: 43046721 Create seed table. 112 secs passed max number of mismatches: read_length * 8% max gap size: 0 kmer cut-off ratio: 5e-07 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4 quality cutoff: 0 base quality char: '!' min fragment size:28 max fragemt size:500 start from read #1 end at read #4294967295 additional alignment: T in reads => C in reference mapping strand (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(4 threads) Input read file #1: CgT3D3_R1a.fastq (format: FASTQ) Input read file #2: CgT3D3_R2a.fastq (format: FASTQ) Output file: bsmap_out_CgT3D3.sam (format: SAM) Thread #3: 200000 read pairs finished. 205 secs passed Thread #2: 150000 read pairs finished. 206 secs passed Thread #1: 100000 read pairs finished. 206 secs passed Thread #0: 50000 read pairs finished. 208 secs passed Thread #3: 250000 read pairs finished. 306 secs passed Thread #2: 300000 read pairs finished. 307 secs passed Thread #1: 350000 read pairs finished. 309 secs passed Thread #0: 400000 read pairs finished. 311 secs passed Thread #3: 450000 read pairs finished. 407 secs passed Thread #2: 500000 read pairs finished. 409 secs passed Thread #1: 550000 read pairs finished. 410 secs passed Thread #0: 600000 read pairs finished. 414 secs passed Thread #3: 650000 read pairs finished. 498 secs passed Thread #2: 700000 read pairs finished. 500 secs passed Thread #1: 750000 read pairs finished. 501 secs passed Thread #0: 800000 read pairs finished. 504 secs passed Thread #3: 850000 read pairs finished. 588 secs passed Thread #2: 900000 read pairs finished. 589 secs passed Thread #1: 950000 read pairs finished. 589 secs passed Thread #0: 1000000 read pairs finished. 602 secs passed Thread #1: 1150000 read pairs finished. 638 secs passed Thread #2: 1100000 read pairs finished. 640 secs passed Thread #3: 1050000 read pairs finished. 643 secs passed Thread #0: 1200000 read pairs finished. 645 secs passed Thread #1: 1250000 read pairs finished. 690 secs passed Thread #2: 1300000 read pairs finished. 691 secs passed Thread #3: 1350000 read pairs finished. 694 secs passed Thread #0: 1400000 read pairs finished. 696 secs passed Thread #1: 1450000 read pairs finished. 737 secs passed Thread #2: 1500000 read pairs finished. 738 secs passed Thread #3: 1550000 read pairs finished. 741 secs passed Thread #0: 1600000 read pairs finished. 744 secs passed Thread #1: 1650000 read pairs finished. 802 secs passed Thread #2: 1700000 read pairs finished. 805 secs passed Thread #3: 1750000 read pairs finished. 808 secs passed Thread #0: 1800000 read pairs finished. 812 secs passed Thread #1: 1850000 read pairs finished. 867 secs passed Thread #2: 1900000 read pairs finished. 870 secs passed Thread #3: 1950000 read pairs finished. 872 secs passed Thread #0: 2000000 read pairs finished. 874 secs passed Thread #1: 2050000 read pairs finished. 922 secs passed Thread #2: 2100000 read pairs finished. 926 secs passed Thread #3: 2150000 read pairs finished. 926 secs passed Thread #0: 2200000 read pairs finished. 930 secs passed Thread #1: 2250000 read pairs finished. 1066 secs passed Thread #2: 2300000 read pairs finished. 1076 secs passed Thread #3: 2350000 read pairs finished. 1080 secs passed Thread #0: 2400000 read pairs finished. 1089 secs passed Thread #1: 2450000 read pairs finished. 1177 secs passed Thread #2: 2500000 read pairs finished. 1181 secs passed Thread #3: 2550000 read pairs finished. 1183 secs passed Thread #0: 2600000 read pairs finished. 1187 secs passed Thread #1: 2650000 read pairs finished. 1290 secs passed Thread #2: 2700000 read pairs finished. 1295 secs passed Thread #3: 2750000 read pairs finished. 1296 secs passed Thread #0: 2800000 read pairs finished. 1302 secs passed Thread #1: 2850000 read pairs finished. 1373 secs passed Thread #3: 2950000 read pairs finished. 1381 secs passed Thread #2: 2900000 read pairs finished. 1382 secs passed Thread #0: 3000000 read pairs finished. 1386 secs passed Thread #1: 3050000 read pairs finished. 1510 secs passed Thread #3: 3100000 read pairs finished. 1511 secs passed Thread #2: 3150000 read pairs finished. 1511 secs passed Thread #0: 3200000 read pairs finished. 1512 secs passed Thread #1: 3250000 read pairs finished. 1577 secs passed Thread #3: 3300000 read pairs finished. 1578 secs passed Thread #2: 3350000 read pairs finished. 1579 secs passed Thread #0: 3400000 read pairs finished. 1580 secs passed Thread #1: 3450000 read pairs finished. 1641 secs passed Thread #3: 3500000 read pairs finished. 1643 secs passed Thread #2: 3550000 read pairs finished. 1643 secs passed Thread #0: 3600000 read pairs finished. 1644 secs passed Thread #1: 3650000 read pairs finished. 1699 secs passed Thread #3: 3700000 read pairs finished. 1702 secs passed Thread #2: 3750000 read pairs finished. 1703 secs passed Thread #0: 3800000 read pairs finished. 1704 secs passed Thread #1: 3850000 read pairs finished. 1745 secs passed Thread #3: 3900000 read pairs finished. 1753 secs passed Thread #0: 4000000 read pairs finished. 1754 secs passed Thread #2: 3950000 read pairs finished. 1756 secs passed Thread #1: 4050000 read pairs finished. 1793 secs passed Thread #3: 4100000 read pairs finished. 1799 secs passed Thread #0: 4150000 read pairs finished. 1801 secs passed Thread #2: 4200000 read pairs finished. 1802 secs passed Thread #1: 4250000 read pairs finished. 1841 secs passed Thread #3: 4300000 read pairs finished. 1848 secs passed Thread #0: 4350000 read pairs finished. 1849 secs passed Thread #2: 4400000 read pairs finished. 1850 secs passed Thread #1: 4450000 read pairs finished. 1889 secs passed Thread #3: 4500000 read pairs finished. 1895 secs passed Thread #0: 4550000 read pairs finished. 1896 secs passed Thread #2: 4600000 read pairs finished. 1897 secs passed Thread #1: 4650000 read pairs finished. 1934 secs passed Thread #3: 4700000 read pairs finished. 1940 secs passed Thread #0: 4750000 read pairs finished. 1941 secs passed Thread #2: 4800000 read pairs finished. 1942 secs passed Thread #1: 4850000 read pairs finished. 1980 secs passed Thread #3: 4900000 read pairs finished. 1986 secs passed Thread #0: 4950000 read pairs finished. 1986 secs passed Thread #2: 5000000 read pairs finished. 1987 secs passed Thread #1: 5050000 read pairs finished. 2025 secs passed Thread #3: 5100000 read pairs finished. 2031 secs passed Thread #0: 5150000 read pairs finished. 2032 secs passed Thread #2: 5200000 read pairs finished. 2034 secs passed Thread #1: 5250000 read pairs finished. 2071 secs passed Thread #3: 5300000 read pairs finished. 2077 secs passed Thread #0: 5350000 read pairs finished. 2079 secs passed Thread #2: 5400000 read pairs finished. 2081 secs passed Thread #1: 5450000 read pairs finished. 2116 secs passed Thread #3: 5500000 read pairs finished. 2122 secs passed Thread #0: 5550000 read pairs finished. 2125 secs passed Thread #2: 5600000 read pairs finished. 2126 secs passed Thread #1: 5650000 read pairs finished. 2162 secs passed Thread #3: 5700000 read pairs finished. 2169 secs passed Thread #0: 5750000 read pairs finished. 2171 secs passed Thread #2: 5800000 read pairs finished. 2173 secs passed Thread #1: 5850000 read pairs finished. 2207 secs passed Thread #3: 5900000 read pairs finished. 2215 secs passed Thread #0: 5950000 read pairs finished. 2217 secs passed Thread #2: 6000000 read pairs finished. 2218 secs passed Thread #1: 6050000 read pairs finished. 2253 secs passed Thread #3: 6100000 read pairs finished. 2261 secs passed Thread #2: 6200000 read pairs finished. 2265 secs passed Thread #0: 6150000 read pairs finished. 2265 secs passed Thread #1: 6250000 read pairs finished. 2298 secs passed Thread #3: 6300000 read pairs finished. 2306 secs passed Thread #2: 6350000 read pairs finished. 2310 secs passed Thread #0: 6400000 read pairs finished. 2311 secs passed Thread #1: 6450000 read pairs finished. 2344 secs passed Thread #3: 6500000 read pairs finished. 2351 secs passed Thread #2: 6550000 read pairs finished. 2357 secs passed Thread #0: 6600000 read pairs finished. 2359 secs passed Thread #1: 6650000 read pairs finished. 2402 secs passed Thread #3: 6700000 read pairs finished. 2410 secs passed Thread #2: 6750000 read pairs finished. 2415 secs passed Thread #0: 6800000 read pairs finished. 2418 secs passed Thread #1: 6850000 read pairs finished. 2453 secs passed Thread #3: 6900000 read pairs finished. 2461 secs passed Thread #2: 6950000 read pairs finished. 2465 secs passed Thread #0: 7000000 read pairs finished. 2467 secs passed Thread #1: 7050000 read pairs finished. 2501 secs passed Thread #3: 7100000 read pairs finished. 2509 secs passed Thread #2: 7150000 read pairs finished. 2513 secs passed Thread #0: 7200000 read pairs finished. 2515 secs passed Thread #0: 7380649 read pairs finished. 2542 secs passed Thread #1: 7250000 read pairs finished. 2544 secs passed Thread #3: 7300000 read pairs finished. 2549 secs passed Thread #2: 7350000 read pairs finished. 2550 secs passed Total number of aligned reads: pairs: 3906464 (53%) single a: 1418844 (19%) single b: 1116765 (15%) Done. Finished at Tue Jul 8 15:00:26 2014 Total time consumed: 2550 secs
In [25]:
lib="CgT3D5"
In [26]:
! {bsmaploc}bsmap \
-a {lib}_R1a.fastq \
-b {lib}_R2a.fastq \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-o bsmap_out_{lib}.sam \
-p 4 \
BSMAP v2.74 Start at: Tue Jul 8 15:00:28 2014 Input reference file: Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa (format: FASTA) Load in 7658 db seqs, total size 557717710 bp. 13 secs passed total_kmers: 43046721 Create seed table. 59 secs passed max number of mismatches: read_length * 8% max gap size: 0 kmer cut-off ratio: 5e-07 max multi-hits: 100 max Ns: 5 seed size: 16 index interval: 4 quality cutoff: 0 base quality char: '!' min fragment size:28 max fragemt size:500 start from read #1 end at read #4294967295 additional alignment: T in reads => C in reference mapping strand (read_1): ++,-+ mapping strand (read_2): +-,-- Pair-end alignment(4 threads) Input read file #1: CgT3D5_R1a.fastq (format: FASTQ) Input read file #2: CgT3D5_R2a.fastq (format: FASTQ) Output file: bsmap_out_CgT3D5.sam (format: SAM) Thread #2: 150000 read pairs finished. 97 secs passed Thread #1: 100000 read pairs finished. 98 secs passed Thread #3: 200000 read pairs finished. 98 secs passed Thread #0: 50000 read pairs finished. 99 secs passed Thread #2: 250000 read pairs finished. 133 secs passed Thread #1: 300000 read pairs finished. 135 secs passed Thread #3: 350000 read pairs finished. 136 secs passed Thread #0: 400000 read pairs finished. 137 secs passed Thread #2: 450000 read pairs finished. 172 secs passed Thread #1: 500000 read pairs finished. 175 secs passed Thread #3: 550000 read pairs finished. 175 secs passed Thread #0: 600000 read pairs finished. 176 secs passed Thread #2: 650000 read pairs finished. 216 secs passed Thread #1: 700000 read pairs finished. 217 secs passed Thread #3: 750000 read pairs finished. 222 secs passed Thread #0: 800000 read pairs finished. 227 secs passed Thread #1: 900000 read pairs finished. 276 secs passed Thread #2: 850000 read pairs finished. 276 secs passed Thread #3: 950000 read pairs finished. 278 secs passed Thread #0: 1000000 read pairs finished. 282 secs passed Thread #1: 1050000 read pairs finished. 314 secs passed Thread #2: 1100000 read pairs finished. 314 secs passed Thread #3: 1150000 read pairs finished. 316 secs passed Thread #0: 1200000 read pairs finished. 320 secs passed Thread #1: 1250000 read pairs finished. 352 secs passed Thread #2: 1300000 read pairs finished. 353 secs passed Thread #3: 1350000 read pairs finished. 354 secs passed Thread #0: 1400000 read pairs finished. 358 secs passed Thread #2: 1500000 read pairs finished. 391 secs passed Thread #1: 1450000 read pairs finished. 391 secs passed Thread #3: 1550000 read pairs finished. 392 secs passed Thread #0: 1600000 read pairs finished. 396 secs passed Thread #2: 1650000 read pairs finished. 428 secs passed Thread #1: 1700000 read pairs finished. 429 secs passed Thread #3: 1750000 read pairs finished. 431 secs passed Thread #0: 1800000 read pairs finished. 434 secs passed Thread #2: 1850000 read pairs finished. 466 secs passed Thread #1: 1900000 read pairs finished. 468 secs passed Thread #3: 1950000 read pairs finished. 469 secs passed Thread #0: 2000000 read pairs finished. 473 secs passed Thread #2: 2050000 read pairs finished. 504 secs passed Thread #1: 2100000 read pairs finished. 506 secs passed Thread #3: 2150000 read pairs finished. 507 secs passed Thread #0: 2200000 read pairs finished. 513 secs passed Thread #2: 2250000 read pairs finished. 543 secs passed Thread #1: 2300000 read pairs finished. 545 secs passed Thread #3: 2350000 read pairs finished. 546 secs passed Thread #0: 2400000 read pairs finished. 551 secs passed Thread #2: 2450000 read pairs finished. 581 secs passed Thread #1: 2500000 read pairs finished. 582 secs passed Thread #3: 2550000 read pairs finished. 584 secs passed Thread #0: 2600000 read pairs finished. 589 secs passed Thread #2: 2650000 read pairs finished. 620 secs passed Thread #1: 2700000 read pairs finished. 621 secs passed Thread #3: 2750000 read pairs finished. 622 secs passed Thread #0: 2800000 read pairs finished. 627 secs passed Thread #2: 2850000 read pairs finished. 657 secs passed Thread #1: 2900000 read pairs finished. 658 secs passed Thread #3: 2950000 read pairs finished. 662 secs passed Thread #0: 3000000 read pairs finished. 670 secs passed Thread #1: 3100000 read pairs finished. 695 secs passed Thread #2: 3050000 read pairs finished. 696 secs passed Thread #3: 3150000 read pairs finished. 699 secs passed Thread #0: 3200000 read pairs finished. 707 secs passed Thread #1: 3250000 read pairs finished. 732 secs passed Thread #2: 3300000 read pairs finished. 733 secs passed Thread #3: 3350000 read pairs finished. 735 secs passed Thread #0: 3400000 read pairs finished. 743 secs passed Thread #1: 3450000 read pairs finished. 768 secs passed Thread #2: 3500000 read pairs finished. 768 secs passed Thread #3: 3550000 read pairs finished. 771 secs passed Thread #0: 3600000 read pairs finished. 779 secs passed Thread #1: 3650000 read pairs finished. 804 secs passed Thread #2: 3700000 read pairs finished. 805 secs passed Thread #3: 3750000 read pairs finished. 807 secs passed Thread #0: 3800000 read pairs finished. 816 secs passed Thread #1: 3850000 read pairs finished. 840 secs passed Thread #2: 3900000 read pairs finished. 841 secs passed Thread #3: 3950000 read pairs finished. 843 secs passed Thread #0: 4000000 read pairs finished. 852 secs passed Thread #1: 4050000 read pairs finished. 877 secs passed Thread #2: 4100000 read pairs finished. 878 secs passed Thread #3: 4150000 read pairs finished. 879 secs passed Thread #0: 4200000 read pairs finished. 887 secs passed Thread #1: 4250000 read pairs finished. 914 secs passed Thread #2: 4300000 read pairs finished. 914 secs passed Thread #3: 4350000 read pairs finished. 915 secs passed Thread #0: 4400000 read pairs finished. 923 secs passed Thread #1: 4450000 read pairs finished. 950 secs passed Thread #2: 4500000 read pairs finished. 952 secs passed Thread #3: 4550000 read pairs finished. 952 secs passed Thread #0: 4600000 read pairs finished. 960 secs passed Thread #1: 4650000 read pairs finished. 988 secs passed Thread #2: 4700000 read pairs finished. 990 secs passed Thread #3: 4750000 read pairs finished. 990 secs passed Thread #0: 4800000 read pairs finished. 997 secs passed Thread #1: 4850000 read pairs finished. 1025 secs passed Thread #2: 4900000 read pairs finished. 1027 secs passed Thread #3: 4950000 read pairs finished. 1028 secs passed Thread #0: 5000000 read pairs finished. 1035 secs passed Thread #1: 5050000 read pairs finished. 1063 secs passed Thread #2: 5100000 read pairs finished. 1065 secs passed Thread #3: 5150000 read pairs finished. 1066 secs passed Thread #0: 5200000 read pairs finished. 1073 secs passed Thread #1: 5250000 read pairs finished. 1101 secs passed Thread #2: 5300000 read pairs finished. 1103 secs passed Thread #3: 5350000 read pairs finished. 1103 secs passed Thread #0: 5400000 read pairs finished. 1110 secs passed Thread #1: 5450000 read pairs finished. 1140 secs passed Thread #2: 5500000 read pairs finished. 1142 secs passed Thread #3: 5550000 read pairs finished. 1142 secs passed Thread #0: 5600000 read pairs finished. 1147 secs passed Thread #1: 5650000 read pairs finished. 1177 secs passed Thread #2: 5700000 read pairs finished. 1179 secs passed Thread #3: 5750000 read pairs finished. 1180 secs passed Thread #0: 5800000 read pairs finished. 1184 secs passed Thread #1: 5850000 read pairs finished. 1214 secs passed Thread #2: 5900000 read pairs finished. 1216 secs passed Thread #3: 5950000 read pairs finished. 1217 secs passed Thread #0: 6000000 read pairs finished. 1223 secs passed Thread #1: 6050000 read pairs finished. 1251 secs passed Thread #2: 6100000 read pairs finished. 1253 secs passed Thread #3: 6150000 read pairs finished. 1253 secs passed Thread #0: 6200000 read pairs finished. 1260 secs passed Thread #1: 6250000 read pairs finished. 1288 secs passed Thread #2: 6300000 read pairs finished. 1290 secs passed Thread #3: 6350000 read pairs finished. 1291 secs passed Thread #0: 6400000 read pairs finished. 1297 secs passed Thread #1: 6450000 read pairs finished. 1327 secs passed Thread #2: 6500000 read pairs finished. 1329 secs passed Thread #3: 6550000 read pairs finished. 1330 secs passed Thread #0: 6600000 read pairs finished. 1336 secs passed Thread #1: 6650000 read pairs finished. 1365 secs passed Thread #2: 6700000 read pairs finished. 1366 secs passed Thread #3: 6750000 read pairs finished. 1367 secs passed Thread #0: 6800000 read pairs finished. 1374 secs passed Thread #1: 6850000 read pairs finished. 1403 secs passed Thread #2: 6900000 read pairs finished. 1403 secs passed Thread #3: 6950000 read pairs finished. 1404 secs passed Thread #0: 7000000 read pairs finished. 1411 secs passed Thread #1: 7050000 read pairs finished. 1440 secs passed Thread #2: 7100000 read pairs finished. 1442 secs passed Thread #3: 7150000 read pairs finished. 1443 secs passed Thread #0: 7200000 read pairs finished. 1449 secs passed Thread #0: 7350645 read pairs finished. 1449 secs passed Thread #1: 7250000 read pairs finished. 1472 secs passed Thread #2: 7300000 read pairs finished. 1473 secs passed Thread #3: 7350000 read pairs finished. 1474 secs passed Total number of aligned reads: pairs: 3946673 (54%) single a: 1329262 (18%) single b: 1076148 (15%) Done. Finished at Tue Jul 8 15:25:02 2014 Total time consumed: 1474 secs
methratio¶
In [29]:
lib="CgM1"
In [31]:
!python {bsmaploc}methratio.py \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-u -z -g \
-o methratio_out_{lib}.txt \
-s {bsmaploc}samtools \
bsmap_out_{lib}.sam \
@ Wed Jul 9 08:48:51 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ... @ Wed Jul 9 08:49:47 2014: reading bsmap_out_CgM1.sam ... [samopen] SAM header is present: 7658 sequences. @ Wed Jul 9 08:56:56 2014: read 10000000 lines @ Wed Jul 9 08:57:22 2014: combining CpG methylation from both strands ... @ Wed Jul 9 08:58:14 2014: writing methratio_out_CgM1.txt ... @ Wed Jul 9 09:11:18 2014: done. total 8562355 valid mappings, 48968967 covered cytosines, average coverage: 1.80 fold.
In [32]:
lib="CgT1D3"
In [33]:
!python {bsmaploc}methratio.py \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-u -z -g \
-o methratio_out_{lib}.txt \
-s {bsmaploc}samtools \
bsmap_out_{lib}.sam \
@ Wed Jul 9 09:11:21 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ... @ Wed Jul 9 09:12:14 2014: reading bsmap_out_CgT1D3.sam ... [samopen] SAM header is present: 7658 sequences. @ Wed Jul 9 09:16:59 2014: combining CpG methylation from both strands ... @ Wed Jul 9 09:17:36 2014: writing methratio_out_CgT1D3.txt ... @ Wed Jul 9 09:28:30 2014: done. total 5964269 valid mappings, 39695564 covered cytosines, average coverage: 1.51 fold.
In [34]:
lib="CgT1D5"
In [35]:
!python {bsmaploc}methratio.py \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-u -z -g \
-o methratio_out_{lib}.txt \
-s {bsmaploc}samtools \
bsmap_out_{lib}.sam \
@ Wed Jul 9 09:28:32 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ... @ Wed Jul 9 09:29:25 2014: reading bsmap_out_CgT1D5.sam ... [samopen] SAM header is present: 7658 sequences. @ Wed Jul 9 09:35:00 2014: combining CpG methylation from both strands ... @ Wed Jul 9 09:35:39 2014: writing methratio_out_CgT1D5.txt ... @ Wed Jul 9 09:49:14 2014: done. total 6801985 valid mappings, 45492773 covered cytosines, average coverage: 1.54 fold.
In [36]:
lib="CgM3"
In [37]:
!python {bsmaploc}methratio.py \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-u -z -g \
-o methratio_out_{lib}.txt \
-s {bsmaploc}samtools \
bsmap_out_{lib}.sam \
@ Wed Jul 9 09:49:16 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ... @ Wed Jul 9 09:50:09 2014: reading bsmap_out_CgM3.sam ... [samopen] SAM header is present: 7658 sequences. @ Wed Jul 9 09:57:03 2014: read 10000000 lines @ Wed Jul 9 09:58:02 2014: combining CpG methylation from both strands ... @ Wed Jul 9 09:58:44 2014: writing methratio_out_CgM3.txt ... @ Wed Jul 9 10:12:52 2014: done. total 9597901 valid mappings, 53820491 covered cytosines, average coverage: 1.79 fold.
In [38]:
lib="CgT3D3"
In [39]:
!python {bsmaploc}methratio.py \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-u -z -g \
-o methratio_out_{lib}.txt \
-s {bsmaploc}samtools \
bsmap_out_{lib}.sam \
@ Wed Jul 9 10:12:54 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ... @ Wed Jul 9 10:13:46 2014: reading bsmap_out_CgT3D3.sam ... [samopen] SAM header is present: 7658 sequences. @ Wed Jul 9 10:21:42 2014: read 10000000 lines @ Wed Jul 9 10:21:59 2014: combining CpG methylation from both strands ... @ Wed Jul 9 10:22:41 2014: writing methratio_out_CgT3D3.txt ... @ Wed Jul 9 10:36:35 2014: done. total 8688793 valid mappings, 52876971 covered cytosines, average coverage: 1.67 fold.
In [40]:
lib="CgT3D5"
In [41]:
!python {bsmaploc}methratio.py \
-d Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \
-u -z -g \
-o methratio_out_{lib}.txt \
-s {bsmaploc}samtools \
bsmap_out_{lib}.sam \
@ Wed Jul 9 10:36:37 2014: reading reference Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ... @ Wed Jul 9 10:37:30 2014: reading bsmap_out_CgT3D5.sam ... [samopen] SAM header is present: 7658 sequences. @ Wed Jul 9 10:46:20 2014: read 10000000 lines @ Wed Jul 9 10:46:33 2014: combining CpG methylation from both strands ... @ Wed Jul 9 10:47:28 2014: writing methratio_out_CgT3D5.txt ... @ Wed Jul 9 11:01:13 2014: done. total 8650035 valid mappings, 52138971 covered cytosines, average coverage: 1.70 fold.
Converting methratio files for methylkit
In [39]:
!cat ./scripts/mr3x.awk
#!/usr/bin/awk -f
!awk {if ($8 >= 3) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}
In [40]:
!cat ./scripts/mr_gg.awk.sh
#!/usr/bin/awk -f
BEGIN{ print "chr.Base\tchr\tbase\tstrand\tcoverage\tfreqC\tfreqT" }
{
if ($3 == "+") {
strand="F"
} else {
strand="R"
}
FC=($7/$8)*100
FT=(1-($7/$8))*100
chrbase=$1"."$2
printf "%s\t%s\t%s\t%s\t%d\t%.2f\t%.2f\n",
chrbase, $1, $2, strand, $8, FC, FT
}
In [23]:
for i in ("CgM1","CgT1D3","CgT1D5", "CgM3", "CgT3D3", "CgT3D5"):
!echo {i}
#!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out_{i}.txt> methratio_out_{i}CG.txt
!awk -f ./scripts/mr3x.awk methratio_out_{i}CG.txt > mr3x.{i}.txt
# can delete !tr ' ' "\t" <mr3x.{i}.txt> mr3_{i}.txt
!awk -f ./scripts/mr_gg.awk.sh mr3x.{i}.txt > mkfmt_{i}.txt
CgM1 CgT1D3 CgT1D5 CgM3 CgT3D3 CgT3D5
Methylkit¶
In [24]:
%pylab inline
Populating the interactive namespace from numpy and matplotlib
In [25]:
%load_ext rpy2.ipython
In [26]:
%R library(methylKit)
Out[26]:
<StrVector - Python:0x101e61440 / R:0x10df9b148> [str, str, str, ..., str, str, str]
In [27]:
%R library(data.table)
data.table 1.9.2 For help type: help("data.table")
In [28]:
%R library(GenomicRanges)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames,
sapply, setdiff, sort, table, tapply, union, unique, unlist
Loading required package: IRanges
Loading required package: XVector
Attaching package: ‘GenomicRanges’
The following object is masked from ‘package:data.table’:
last
In [29]:
ls mkfmt*
mkfmt_CgM1.txt mkfmt_CgM3.txt mkfmt_CgT1D3.txt mkfmt_CgT1D5.txt mkfmt_CgT3D3.txt mkfmt_CgT3D5.txt mkfmt_CgM1txt mkfmt_CgM3txt mkfmt_CgT1D3txt mkfmt_CgT1D5txt mkfmt_CgT3D3txt mkfmt_CgT3D5txt
In [34]:
%%R file.list <- list
('mkfmt_CgM1.txt',
'mkfmt_CgT1D3.txt',
'mkfmt_CgT1D5.txt',
'mkfmt_CgM3.txt',
'mkfmt_CgT3D3.txt',
'mkfmt_CgT3D5.txt'
)
In [37]:
%R myobj=read(file.list,sample.id=list("1_sperm","1_72hpf","1_120hpf","2_sperm","2_72hpf","2_120hpf"),assembly="v9",treatment=c(0,0,0,1,1,1))
Out[37]:
<ListVector - Python:0x10ad4cea8 / R:0x111945910> [ListV..., ListV..., ListV..., ListV..., ListV..., ListV...] <ListVector - Python:0x10ad4cea8 / R:0x111945910> [ListV..., ListV..., ListV..., ListV..., ListV..., ListV...] <ListVector - Python:0x10ad4cea8 / R:0x111945910> [ListV..., ListV..., ListV..., ListV..., ListV..., ListV...] <ListVector - Python:0x10ad4cea8 / R:0x111945910> [ListV..., ListV..., ListV..., ListV..., ListV..., ListV...] <ListVector - Python:0x10ad4cea8 / R:0x111945910> [ListV..., ListV..., ListV..., ListV..., ListV..., ListV...] <ListVector - Python:0x10ad4cea8 / R:0x111945910> [ListV..., ListV..., ListV..., ListV..., ListV..., ListV...] <ListVector - Python:0x10ad4cea8 / R:0x111945910> [ListV..., ListV..., ListV..., ListV..., ListV..., ListV...]
In [38]:
%%R
meth<-unite(myobj)
head(meth)
nrow(meth)
getCorrelation(meth,plot=T)
hc<- clusterSamples(meth, dist="correlation", method="ward", plot=T)
PCA<-PCASamples(meth)
1_sperm 1_72hpf 1_120hpf 2_sperm 2_72hpf 2_120hpf
1_sperm 1.0000000 0.8206750 0.8113192 0.7849752 0.7860873 0.7850139
1_72hpf 0.8206750 1.0000000 0.8107486 0.8127752 0.8181483 0.8197261
1_120hpf 0.8113192 0.8107486 1.0000000 0.8055833 0.8133956 0.8110224
2_sperm 0.7849752 0.8127752 0.8055833 1.0000000 0.8652725 0.8636885
2_72hpf 0.7860873 0.8181483 0.8133956 0.8652725 1.0000000 0.8623747
2_120hpf 0.7850139 0.8197261 0.8110224 0.8636885 0.8623747 1.0000000
In []: