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sr320 / LabDocs

Roberts Lab Documents
http://sr320.github.io/LabDocs/
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Analyze C. virginica BS samples #590

Closed sr320 closed 7 years ago

sr320 commented 7 years ago

Take our own C. virginica Bisulfite samples and run "Methylation" pipeline to identify DMRs.

getting raw files will be test of our DMP :)

Genome is at https://www.ncbi.nlm.nih.gov/nuccore/MWPT00000000.1/

sr320 commented 7 years ago

I get about 20% mapping with bsmap https://github.com/sr320/nb-2017/blob/master/C_virginica/04-Cvirg-BS-Cvirg-NCBI.ipynb

seanb80 commented 7 years ago

I'm re-running Bismark with some better trimmed data, will also try it with BSMap to see if we can get at least similar results, if not better.