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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Bug: the wrong peak called by macs2 #487

Open ZHIDIHUAYUAN opened 2 years ago

ZHIDIHUAYUAN commented 2 years ago

Hi: I used the MACS2 to deal with the ATAC-seq. The command was macs2 callpeak -t /Sh4-1.chr_filt_dedup_sortbyname_fixed_tn5.bedpe -f BEDPE -n Sh4-1 -g hs --outdir ./ -B --keep-dup all --call-summits

The output of Sh4-1_peaks.narrowPeak contains: chr19 41714971 41721180 test_Sh4-1_peak_12088 4605 . 8.66483 464.632 460.565 3281 But the bw shown in IGV: image It seems that there were multiple peaks rather that one peak. What is wrong? Please help me. Thank you

taoliu commented 2 years ago

@ZHIDIHUAYUAN I think you just piled up the "tags" / read ends of ATAC-seq to make these signal tracks in IGV since the file name ends with '.bam.bw'. In MACS, the whole fragment defined in '.bedpe' will be piled up so if you want to figure out what MACS 'sees', you can use 'bedtools genomecov' on the '.bedpe' file or simply let MACS generate 'bedGraph' with -B option and load it into IGV. Please update me when you get the MACS piled up signal into IGV.

ZHIDIHUAYUAN commented 2 years ago

@taoliu Thanks for your help. I got the Sh4-1_control_lambda.bdg and Sh4-1_treat_pileup.bdg into IGV. The results were shown as follows: image I also checked the peak again. image It seems that this peak was too long.