pyth

./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/Mollusk/BSMAPoutput_174gm_v9_90.sam -p 8

http://eagle.fish.washington.edu/Mollusk/174gm%20analysis/BSMAPoutput_174gm_v9_90.sam

./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

python methratio.py -d /Volumes/web/whale/ce_bs/oyster.v9_90.fa -o /Volumes/web/Mollusk/methratiopython_174gm_v9_90.txt -s /Users/Shared/Apps/bsmap-2.73/samtools -z -u /Volumes/web/Mollusk/174gm_analysis/BSMAPoutput_174gm_v9_90.sam

total 145949462 valid mappings, 123681367 covered cytosines, average coverage: 11.86 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.