Question: How to use MACS2 to do peak calling
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gravatar for mikysyc2016
14 months ago by
mikysyc201650
mikysyc201650 wrote:

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 • 1.7k views
ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 14 months ago by mikysyc201650

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 REPLYlink written 14 months ago by h.mon27k

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 REPLYlink written 14 months ago by mikysyc201650
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