Question: How to use MACS2 to do peak calling
gravatar for mikysyc2016
2.1 years ago by
mikysyc201670 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. 2.


chip-seq • 3.2k views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 2.1 years ago by mikysyc201670

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 2.1 years ago by h.mon30k

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 2.1 years ago by mikysyc201670
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