How to use MACS2 to do peak calling

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6.5 years ago

mikysyc2016 ▴ 120

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 • 7.6k views

ADD COMMENT • link updated 6.4 years ago by Biostar 20 • written 6.5 years ago by mikysyc2016 ▴ 120

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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.

ADD REPLY • link 6.5 years ago by h.mon 35k

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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?

ADD REPLY • link 6.5 years ago by mikysyc2016 ▴ 120

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