Question: DESeq on CCAT identified chipseq peaks
3.0 years ago by
Guest User • 12k
Guest User • 12k wrote:
I plan on using DESeq downstream of CCAT identified peaks on 5 tumor and 5 normal samples and I was unsure of how to best create a unified list of peaks and corresponding read counts - CCAT outputs different peak regions from each sample. Thus to create a unified list of peak regions and their read counts would you suggest - A. Taking a union of all the CCAT called peaks and calculating read count in each biological replicate OR B. Calculating the read count for each peak in each replicate whether or not it has been called in the replicate or not I saw both being suggested earlier online and I am not sure which is appropriate. 2. Since this is chipseq and not rna seq data, do you agree that using coverageBed ( coverageBed -abam $bamfile -b $CCATpeaks > countdata) would work as good as HTseqcount ? Thanks ! -- output of sessionInfo(): - -- Sent via the guest posting facility at bioconductor.org.
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