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Posts by Haibo.Liu
... Please refer to my git hub scripts: https://github.com/seaYali/ATACseqQC/blob/master/ScriptsForATACseqQCCaseStudy.txt for your analysis. Currently, the bottle neck of this package is the BamQC.R function. I did this step using samtools instead for efficinecy. Importantly, for the purpose of QC, You ...
... Yes, ChIPpeakAnno will do the job for you. First treat your defined range windows as ChIP peak ranges (for input format, see the manual of ChIPpeakAnno). Then convert the ranges to a GRanges object with toGRanges() function. peaks <- toGRanges(yourfile, format="broadPeak") ## your file is the ...
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