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bigWig tracks inconsistent with MACS2 callpeak

Hi, all

Recently, I have been dealing with some H3K27me3 ChIP-seq data. I used MACS2 to callpeak (with --broad ) and visualized the bw files (converted from bam) in IGV.

For me, this entire window seems possessed H3K27me3 modification, but the MACS2 just take the high signal region as H3K27me3 peak.

What I want to do is to get genes with H3K27me3 modification. If I take MACS2 as reference it may overlook some genes with low level H3K27me3 modification.

My question is how do yours handling this broad peak issues? Do we have better peakcallers for broad peaks like H3K27me3?

Thanks in advance

Lida

chip-seq macs2
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written by lida • lida

Can you post your full MACS2 command, and are any of those tracks input or some sort of negative control?

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written by rpolicastro rpolicastro

Sure, my MACS2 command is macs2 callpeak -t <IP.bam> -c <Input.bam> -f BAM -g dm -p 0.01 -B --outdir macs_res --min-length 3000 --nomodel --extsize 300 --broad

This is input 1-5.scale.bw) and IP 11-15.scale.bw) samples

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written by lida • lida

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