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3 questions
1
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1
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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 ...
- 343
1
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2
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127
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How to extract DNA sequence from browser track input files (BigWig, bed etc.) files
A BigWig file for something like Chip-seq, or ATAC data has the following format for each line i:
chrom_i - start_i - end_i - value_i
I need to convert for each line the (start_i -> end_i) ...
- 343
0
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1
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149
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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 ...
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