Questions tagged [peak-calling]
The peak-calling tag has no usage guidance.
18
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What is the required input peak file format for IDR (Irreproducible Discovery Rate)
I have managed to install IDR (https://github.com/nboley/idr) correctly (idr --version returns 2.0.3), but I can't get it to run on my peak files (*.bed) without crashing.
My peak files are generated ...
- 323
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125
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chip seq biological replicate merge after peak-calling
I have 3 biological replicates for KO condition. What I have done so far
Peak calling
The removed blacklisted region
Now Im bit confused about the peak merging stage. Here Im trying to use the ...
- 1,754
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141
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How to interpret track height in Chipseq?
I recently received some .bigwig files from a chipseq experiment.
I loaded the files into IGV.
The interpretation is rather intuitive.
My question is the following:
What exactly do the track heights ...
- 237
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annotation using ChIPseeker package error
I have differential binding sites object obtain from diffBind (dba.report). I am using the ChIP Seeker package to annotate the peaks but keep getting the following error: Error in (function (classes, ...
- 95
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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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How to calculate the number of peaks that are upstream/downstream of some other peaks
I have 3 histone marks,I have used Macs2 for peak calling and diffBind to analyze the peaks. I was wondering if you know any way to calculate the peak numbers of one specific histone mark that occur ...
- 95
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188
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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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Hypergeometic test for the overlap of two set of genomic intervals (e.g. from Chip-seq data)
Suppose I have done two Chip-seq experiments. Now after the bias correction step such as MACS2, I get two set of genomic intervals (or peaks, as what is usually called) that corresponds to each of the ...
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345
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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 ...
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697
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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 ...
- 331
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366
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Peak-calling using homer
I have a total of 78 ATAC seq samples from which Im trying to do a peak call .I tried this batchParallel.pl findPeaks peaks function but i couldn't find the output ...
- 1,754
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266
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How to handle control samples in CLIP-Seq
I have a CLIP-Seq dataset I'm processing, which includes control samples and no inputs. This is the second CLIP analysis I've performed to help out users of our genome core facility and the first one ...
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55
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What are the mathematical assumptions and algorithmic procedure behind MACS2?
I wonder if there's some mathematical details that outline what the algorithms does.
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Occupancy of TFs with the target genes
The occupancy of SMARCD3 in the target genes listed below. I want to see average, normalized ChIP-seq signal at the promoter proximal region (1000bp upstream and downstream of the TSS).
I have 4 ...
- 1,754
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Detecting broad peaks in sRNA-seq data
What kind of tool would be appropriate do detect "broad peaks" in small RNA-seq sequencing data?
MACS2 appears to be developed for ChIP-seq data, but I see that there is a ...
- 3,090
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176
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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 ...
- 2,133
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determine if ChIP-seq peaks are broad or narrow
Is there a method to determine if the peaks are broad or narrow? ENCODE provides some guidelines:
Although those cover common histone marks, there are many others. If you are using one of the ones ...
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151
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Finding peaks and estimating cell population sizes in multi-dimensional flow cytometry data
Our research institute processes a lot of flow cytometry data, but the produced data is under-utilised due to the effort required to process it. A typical run will produce 5 million events (ideally ...
- 13.5k