Workflow: Analysis of BSMAP data

This workflow outlines analysis of data from mapping bisulfite treated DNA (BS-seq) to the oyster genome.

Initially sequencing reads, in this case from oyster sperm, are mapped to the genome using BS-MAP.

code ./bsmap -a /Volumes/betty/filtered_174gm_A_NoIndex_L006_R1.fastq.gz -b /Volumes/betty/filtered_174gm_A_NoIndex_L006_R2.fastq.gz -d /Volumes/betty/oyster_v9.fa -o /Volumes/betty/BiGO_Betty_plain.sam -p 4

output Total number of aligned reads: pairs: 90102067 (53%) single a: 17033002 (9.9%) single b: 15975991 (9.3%)