Questions tagged [macs2]

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592 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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1answer
116 views

ATAC-seq macs2 peak splitting in sliding windows

This question has also been asked on Biostars 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 ...
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3answers
91 views

differential analysis of chip-seq data

I have several sets of chip-seq data. I called the peaks using Macs2. I am pretty new to the field and I will appreciate any help. I wanted to annotate the peaks and see which peaks are shared between ...
1
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1answer
775 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. ...
1
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1answer
109 views

When running ChIPQC bioconductor package after peak calling, should I use sorted BAM files or unsorted 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 BAM files? I have created sorted BAM files ...
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2answers
31 views

Separating peaks of chip-seq with specific length

My data contain several chip-seq results. I have the peaks called by MACS2.I wanted to only look at those peaks that their size is e.g 500bp to 1000bp. How can I separate those peaks efficiently? I ...
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2answers
116 views

How to make Venn diagram for the Macs peak calling output of two data sets?

I have two outputs of macs2 peak calling for two of my data sets. I wanted to plot the Venn diagram to see how many peaks are shared. I mainly work on Unix/Linux. Do you know any way that I can have ...
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2answers
2k views

merging two/or more bed file into one bed file

I am trying to merge two bed files (more in future) to one. my bed files are something like : . I need to merge them in a way to have the shared chromosome location. Is there a way to do that ?
1
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1answer
229 views

How to get the intersection of peaks after peak calling using MACS2?

I have following 5 narrow peak files after peak calling. K14_peaks.narrowPeak K15_peaks.narrowPeak K16_peaks.narrowPeak K3_peaks.narrowPeak K8_peaks.narrowPeak I ...
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1answer
54 views

gnu parallel for macs peak calling

These are the list of files ...
1
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2answers
470 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 ...
1
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1answer
95 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 ...