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Old 10-26-2017, 06:45 AM   #1
Hedi86
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Location: Norway

Join Date: Oct 2017
Posts: 23
Question Workflow and setting in Seqmonk

Dear all

im going to analyze bisulfite sequencing data and determine the DMR in my test and treatment groups. here is my workflow and setting for SeqMonk software but im not sure whether they are correct or not. i am specifically asking about those values inside parenthesis (i took them from a course material provided by Babraham Inst).


Import data > bismark(cov) > Edit replicate sets > Define probes > read position probe generator > minimum read account per position (1) and valid position per window (100) > quantitate existing probe > enrichment qualification > quantitation pipelines > Bisulphite methylation over feature > minimum count to include position (1) > minimum observations to include feature (10) > filter on value difference > difference in quantitated value > must be between (25) and empty > filter by statistical test > replicate set stats > p value cutoff 0.01 and apply multiple correction

thank you so much for your help.
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