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
###One of the first points of information that we are interested in is how many CpG loci is there information for?
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
