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.
./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%)
http://eagle.fish.washington.edu/cnidarian/BiGO_Betty_plain.sam
Resulting SAM file then subjected to methratio python script
python methratio.py -d /Volumes/betty/oyster_v9.fa -u -z -g -o /Volumes/betty/BiGO_betty_plain_methratio_v1.txt -s /Volumes/Bay3/Software/BSMAP/bsmap-2.73/samtools /Volumes/betty/BiGO_Betty_plain.sam
output:
total 167774088 valid mappings, 127192776 covered cytosines, average coverage: 13.23 fold.
http://eagle.fish.washington.edu/cnidarian/BiGO_betty_plain_methratio_v1.txt
This file was uploaded to SQLShare using python script
python singleupload.py sr320@washington.edu c8APIKEYAPIKEYAPIKEY5c15c /Volumes/web/cnidarian/BiGO_betty_plain_methratio_v1.txt
The following query will get all lines where CG are in the 3rd and 4th position.
SELECT * FROM [sr320@washington.edu].[BiGO_betty_plain_methratio_v1.txt] betty where context like '__CG_' --_=single character wildcard
<img src="https://www.evernote.com/shard/s10/sh/ea1d91af-c92b-4461-a979-c357dce141ff/285518308334e0dfb6eed38f1eb2902e/deep/0/Screenshot%205/24/13%2010:45%20AM.png" width = "60%" "alt="Screenshot%205/24/13%2010:45%20AM" />
In this case will make GFF only of CpGs, where there is at least 10x coverage.
more soon