TJGR PE Gonad BS

./bsmap -a /Volumes/Bay4\ scratch/temp/filtered_Unlabeled_NoIndex_L003_R1wID_trimmed.fastq -d /Volumes/NGS\ Drive/Oyster\ Genome/oyster.v9_M.fa -o /Volumes/AquaculX/armina/BSMAP_output_trimmed_v9_M.sam -p 2

hummingbird

./bsmap -a /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/web/whale/ce_bs/oyster.v9_90.fa -o /Volumes/web/whale/ce_bs/BSMAP_output_PE_v9_90.sam -p 8

note: can run gunzipped fastq

Total number of aligned reads:

pairs: 85147571 (50%)

single a: 16704916 (9.7%)

single b: 15703005 (9.2%)

Done.

Finished at Thu Dec 20 10:31:38 2012

running methratio on greenbird

python methratio.py -d /Volumes/web/whale/ce_bs/oyster.v9_90.fa -u -p -q -z -o /Volumes/web/whale/ce_bs/OUT_methratio_gonadPE_v9_90_A.txt -s /Volumes/Bay3/Software/samtools /Volumes/web/whale/ce_bs/BSMAP_output_PE_v9_90.sam

total 136437582 valid mappings, 119535479 covered cytosines, average coverage: 11.15 fold.

python methratio.py -d /Volumes/web/whale/ce_bs/oyster.v9_90.fa -u -p -q -z -o /Volumes/web/whale/ce_bs/OUT_methratio_gonadPE_v9_90_B.txt -s /Users/Shared/Apps/bsmap-2.73/samtools /Volumes/web/whale/ce_bs/BSMAP_output_PE_v9_90.sam

total 136437582 valid mappings, 119535479 covered cytosines, average coverage: 11.15 fold.

Filter for + only

~63,000,000 lines

format: tabular, database: ?

Info: Filtering with c3=='+',

kept 50.01% of 119535480 valid lines (119535480 total lines).

trim col 4, the select CG

example

#C+T >/= 10

@3.6 million

http://eagle.fish.washington.edu/cnidarian/TJGR_GonadPE_BS_v9_90_CG_10x.txt

WORKFLOW

http://eagle.fish.washington.edu/cnidarian/Galaxy-Workflow-methratio_processing.ga

complete wf

http://eagle.fish.washington.edu/cnidarian/Galaxy-Workflow-methratio_processing_BED.ga

methylated

~940,000 lines

format: tabular, database: ?

Info: Filtering with c5>0,

kept 26.97% of 3571019 valid lines (3571019 total lines).

http://eagle.fish.washington.edu/cnidarian/TJGR_GonadPE_BS_v9_90_CG_10x_METHbed.txt

http://eagle.fish.washington.edu/cnidarian/TJGR_GonadPE_BS_v9_90_CG_10x_NOmethbed.txt

Methylated CGs that overlap with CDS

abort- writing lot data to terminal

BSMAP v2.73

Start at: Thu Dec 20 11:56:09 2012

Input reference file: /Volumes/web/whale/ce_bs/oyster.v9_90.fa (format: FASTA)

Load in 1670 db seqs, total size 502809129 bp. 12 secs passed

total_kmers: 43046721

Create seed table. 32 secs passed

max number of mismatches: 5 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: 2 base quality char: '!'

min fragment size:28 max fragemt size:300

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(8 threads)

Input read file #1: /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R1.fastq.gz (format: gzipped FASTQ)

Input read file #2: /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R2.fastq.gz (format: gzipped FASTQ)

Output file: /Volumes/web/whale/ce_bs/BSMAP_output_PE_v9_90_C.sam (format: SAM)

Total number of aligned reads:

pairs: 87768222 (51%)

single a: 18091279 (11%)

single b: 16521277 (9.6%)

./bsmap -a /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/web/whale/ce_bs/oyster.v9_M.fa -o /Volumes/web/whale/ce_bs/BSMAP_output_PE_v9_M_A.sam -p 6

Total number of aligned reads:

pairs: 32019169 (19%)

single a: 9632050 (5.6%)

single b: 9262145 (5.4%)

Done.

./bsmap -a /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/web/whale/ce_bs/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/web/whale/ce_bs/oyster.v9.fa -o /Volumes/web/whale/ce_bs/BSMAP_output_PE_v9_A.sam -p 8 -x 300 -q 2 -w 100 -v 5

complete

Total number of aligned reads:

pairs: 93132679 (54%)

single a: 17844205 (10%)

single b: 16710672 (9.7%)

Done.

python methratio.py -d /Volumes/web/whale/ce_bs/oyster.v9_90.fa -u -p -q -z -o /Volumes/web/whale/ce_bs/OUT_methratio_gonadPE_v9_90_C.txt -s /Users/Shared/Apps/bsmap-2.73/samtools /Volumes/web/whale/ce_bs/BSMAP_output_PE_v9_90_D.sam