How to use MACS2 to do peak calling · Biostar

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How to use MACS2 to do peak calling

Hi all, I see two website to introduce MACS. Now i have a bam file which one I should use? I attach them below: 1. https://hbctraining.github.io/In-depth-NGS-Data-Analysis-Course/sessionV/lessons/03_peak_calling_macs.html 2. https://github.com/taoliu/MACS/wiki/Advanced:-Call-peaks-using-MACS2-subcommands

Thanks!

chip-seq

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updated 8.1 years ago by Biostar

• written 8.2 years ago by mikysyc2016

Read both. The first is a standard MACS2 workflow and you probably want to follow it for your analysis. The second is a detailed workflow to allow users to tweak MACS2 to several scenarios, it is interesting to learn what callpeak is doing.

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written 8.2 years ago by h.mon

For the first website, the most important command should be: "$ macs2 callpeak -t bowtie2/H1hesc_Nanog_Rep2_chr12_aln.bam -c bowtie2/H1hesc_Input_Rep2_chr12_aln.bam -f BAM -g 1.3e+8 --outdir macs2 -n Nanog-rep2", But the second website has several subcommands( and sometimes need to change certain parameters). Do not know why the first one use much less command can get the same results?

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written 8.2 years ago by mikysyc2016

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