Hi all, I use macs2 to do peak calling for my ChIP-seq results, and use narrowpeak file to run homer with bedgraph file. Please see below. $ annotatePeaks.pl '/home/Desktop/B6KOg/B6KOg_s_2_ACAGTG_peaks.narrowPeak' mm9 -size 400 -bedGraph '/home/Desktop/B6KOg/B6KOg_s_2_ACAGTG_treat_pileup.bdg' '/home/yachen/Desktop/B6KOg/B6KOg_s_2_ACAGTG_control_lambda.bdg' -raw > Desktop/outputB6KOg.txt Then i get a txt file and last two column show me (B6KOg_s_2_ACAGTG_treat_pileup.bdg bedGraph avg over 400 bp) and (B6KOg_s_2_ACAGTG_control_lambda.bdg bedGraph avg over 400 bp). do they means o get tag count for treat peaks and input peaks? or DO you know how to use macs2 to get tag count for samples directly? Thanks!
Question: A question about Homer ChIP-seq analysis
2.1 years ago by
mikysyc2016 • 70
mikysyc2016 • 70 wrote:
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