Questions tagged [macs2]
The macs2 tag has no usage guidance.
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6 views
Methods to analyze MeDIP-seq data
I have MeDIP-seq data. I have 6 groups with 15 replicates and a total of 90 human samples. I am trying to choose the best method to analyze them. I would highly appreciate if you can give me your ...
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2answers
26 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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36 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 ...
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16 views
How to calculate overlapping between different chip-seq peaks
I have 3 sets of data for peaks called by Macs2 as below:
1-DNA methylation
2-Chip-seq (repression marks)
3-Chip-seq (activation marks)
I need to show how many peaks in DNA methylation have the same ...
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2answers
41 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
222 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
60 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
32 views
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1answer
31 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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1answer
230 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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0answers
22 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
66 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
336 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
242 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
vote
1answer
76 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 ...
