Questions tagged [macs2]
The macs2 tag has no usage guidance.
12
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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 ...
- 95
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3
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120
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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 ...
- 95
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151
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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 ...
- 95
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3k
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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 ?
- 95
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314
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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 ...
- 321
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60
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1
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1
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126
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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 ...
- 321
1
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976
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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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- 321
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123
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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 ...
- 11
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2
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681
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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 ...
- 111
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545
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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 ...
- 11
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104
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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 ...
- 2,073