Question: A question about Homer ChIP-seq analysis
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gravatar for mikysyc2016
8 months ago by
mikysyc201630
mikysyc201630 wrote:

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!

chip-seq • 404 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by mikysyc201630

Are you asking how to count the number of reads aligned within peak regions? If so, you can do this with Bedtools:

bedtools map -a peaks.bed -b coverage.bedgraph -c 4 -o mean
ADD REPLYlink written 8 months ago by James Ashmore2.6k

Thanks. I use two file from macs2 analysis (one is file:ko1_2.72_summits.bed, another is ko1_2.72_treat_pileup.bdg) as bed and bedgraph as you mentioned, but i get error as below: ERROR: chromomsome sort ordering for file ko1_0.01_q/ppara_ko1_2.72_treat_pileup.bedgraph is inconsistent with other files. Do you know why this happen?

ADD REPLYlink modified 8 months ago • written 8 months ago by mikysyc201630

Bedtools expects both files to be sorted in the same order. Sort both files by chromosome and start position:

sort -k1,1 -k2,2n coverage.bedgraph > coverage_sorted.bedgraph
sort -k1,1 -k2,2n peaks.bed > peaks_sorted.bed
ADD REPLYlink modified 8 months ago • written 8 months ago by James Ashmore2.6k

It works. Thank you.

ADD REPLYlink written 8 months ago by mikysyc201630
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