Questions tagged [macs2]

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When running ChIPQC bioconductor package after peak calling, should I use sorted BAM files or unsorted original BAM files?

I have called peaks using MACS2 and now I'm trying to run ChIPQC bioconductor package. Can someone please tell me should I use sorted BAM files or unsorted original BAM files? I have created sorted ...
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1answer
33 views

How to visualize called narrowPeak files in UCSC Genome browser or IGV?

I have called peaks using MACS2. Then I got a narrowPeak file like this. ...
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16 views

How to decide the parameters and parameter values when running ChIP-seq Peak Calling for H3K27ac data in MACS?

I have alignment data in SAM files from ChIP-seq analysis for H3K27ac mark. I need to call peaks using MACS2. But I'm having issues with selecting parameters and values of the parameters. I will be ...
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2answers
44 views

ATAC-seq macs2 peak splitting in sliding windows

I used macs2 to call peaks for atac-seq data. now my goal is to split the peaks into 50 bp windows with 25 bp steps and then calculate the Tn5 integration frequency in each window. How should I ...
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1answer
160 views

Convert paired-end BAM into a single-end BAM and keep all the reads

I want to call peaks using MACS2 on my paired-end ATAC-seq BAM and I am interested in cutting sites. So I make use of the -BAM option (opposed to the -BAMPE) option. However this throws away all the ...
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2answers
117 views

Biological replicates on Chip-seq Transcription factor data

I have 2 biological replicates for chip-seq transcription factor data and I have applied macs2 peak calling for each replicate separately. How can i make use of the biological replicates to extract ...
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1answer
57 views

Score predefined ChIP-seq peaks with MACS2 or equivalent

I have performed peak calling on a number of separate ChIP-seq experiments and would like to harmonise the peaks from each of the experiments in order to convert my data into a matrix for further ...