Running Genome Prep on genefish, and greenbird
Genome prep complete
will try
robertsmac:bismark_v0.7.12 sr320$ ./bismark -n 1 -l 50 ./genome/ -1 /Volumes/Bay3/Software/bismark_v0.7.12/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -2 /Volumes/Bay3/Software/bismark_v0.7.12/filtered_174gm_A_NoIndex_L006_R2.fastq.gz
./bismark -n 1 -l 50 ./genome/ -1 /Volumes/Bay3/Software/bismark_v0.7.12/filtered_174gm_A_NoIndex_L006_R1.fastq -2 /Volumes/Bay3/Software/bismark_v0.7.12/filtered_174gm_A_NoIndex_L006_R2.fastq --path_to_bowtie /Volumes/Bay3/Software/bowtie/
./bismark -n 1 -l 50 ./genome/ /Volumes/Bay3/Software/bismark_v0.7.12/filtered_174gm_A_ACTGATA_L002_R1.fastq --path_to_bowtie /Volumes/Bay3/Software/bowtie/
Was able to get QC run (non compressed) file to run
# reads processed: 1716124
# reads with at least one reported alignment: 605830 (35.30%)
# reads that failed to align: 1110294 (64.70%)
Reported 887012 alignments to 1 output stream(s)
# reads processed: 1716124
# reads with at least one reported alignment: 606261 (35.33%)
# reads that failed to align: 1109863 (64.67%)
Reported 887483 alignments to 1 output stream(s)
Processed 1716124 sequences in total
Successfully deleted the temporary file filtered_174gm_A_ACTGATA_L002_R1.fastq_C_to_T.fastq
Final Alignment report
======================
Sequences analysed in total: 1716124
Number of alignments with a unique best hit from the different alignments: 542030
Mapping efficiency: 31.6%
Sequences with no alignments under any condition: 807900
Sequences did not map uniquely: 366194
Sequences which were discarded because genomic sequence could not be extracted: 24
Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT: 271229 ((converted) top strand)
CT/GA: 270801 ((converted) bottom strand)
GA/CT: 0 (complementary to (converted) top strand)
GA/GA: 0 (complementary to (converted) bottom strand)
Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
Final Cytosine Methylation Report
=================================
Total number of C's analysed: 3153457
Total methylated C's in CpG context: 60447
Total methylated C's in CHG context: 240
Total methylated C's in CHH context: 810
Total C to T conversions in CpG context: 312791
Total C to T conversions in CHG context: 550803
Total C to T conversions in CHH context: 2228366
C methylated in CpG context: 16.2%
C methylated in CHG context: 0.0%
C methylated in CHH context: 0.0%
This should work now
./bismark -n 1 -l 50 ./genome/ -1 /Volumes/Bay3/Software/bismark_v0.7.12/filtered_174gm_A_NoIndex_L006_R1.fastq -2 /Volumes/Bay3/Software/bismark_v0.7.12/filtered_174gm_A_NoIndex_L006_R2.fastq --path_to_bowtie /Volumes/Bay3/Software/bowtie/
Final Alignment report
======================
Sequence pairs analysed in total: 171582441
Number of paired-end alignments with a unique best hit: 43557152
Mapping efficiency: 25.4%
Sequence pairs with no alignments under any condition: 115765394
Sequence pairs did not map uniquely: 12259895
Sequence pairs which were discarded because genomic sequence could not be extracted: 1785
Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT: 21794732 ((converted) top strand)
GA/CT/CT: 0 (complementary to (converted) top strand)
GA/CT/GA: 0 (complementary to (converted) bottom strand)
CT/GA/GA: 21762420 ((converted) bottom strand)
Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
Final Cytosine Methylation Report
=================================
Total number of C's analysed: 1106419763
Total methylated C's in CpG context: 22049616
Total methylated C's in CHG context: 215158
Total methylated C's in CHH context: 663786
Total C to T conversions in CpG context: 114803767
Total C to T conversions in CHG context: 193101823
Total C to T conversions in CHH context: 775585613
C methylated in CpG context: 16.1%
C methylated in CHG context: 0.1%
C methylated in CHH context: 0.1%
robertsmac:bismark_v0.7.12 sr320$