All Questions
Tagged with macs2 peak-calling
6 questions
1
vote
1
answer
192
views
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 ...
- 343
0
votes
2
answers
52
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 ...
- 125
0
votes
3
answers
212
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 ...
- 125
0
votes
2
answers
556
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 ...
- 125
1
vote
1
answer
1k
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 ...
- 361
1
vote
1
answer
215
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 ...
- 2,173