Merge bigwig Files with different intervals
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6 weeks ago
pt.taklifi ▴ 60

Hello everyone, I am trying to merge about [700 ATAC seq][1] bigwig files together and calculate mean read counts in all intervals. these bigwig files are already normalized , however intervals are not the same in every file. I was wondering if I could calculate read counts in intervals ( coverages) using UCSC bigWigMerge .
Thank you

bigwig Merge • 125 views
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Yes, I think so. Have you tried it ?

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does bigWigMerge simply add read counts in intervals or does it report the mean read count ?

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By default, it reports the sum, but there are other options.

bigWigMerge v2 - Merge together multiple bigWigs into a single output bedGraph.
You'll have to run bedGraphToBigWig to make the output bigWig.
The signal values are just added together to merge them
usage:
   bigWigMerge in1.bw in2.bw .. inN.bw out.bedGraph
options:
   -threshold=0.N - don't output values at or below this threshold. Default is 0.0
   -adjust=0.N - add adjustment to each value
   -clip=NNN.N - values higher than this are clipped to this value
   -inList - input file are lists of file names of bigWigs
   -max - merged value is maximum from input files rather than sum
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I usually use bedtools unionbedg for this, but it requires to first make bedGraphs from bigwig, and then convert back to bigwig. Still, the easiest solution I came across so far. A: Compute average score across multiple bed files

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Deeptools bigwigcompare allows many different operations (log2, ratio, subtract, add, mean, reciprocal_ratio, first, second), along with the optional use of pseudocounts and/or scaling. This is my favorite tool to play with bigwigs.

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But that only goes for two files, does it?

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oh yes you are right

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pt.taklifi Do you really have 700 bigwigs? What kind of experiment is that, it sounds excessive. Not sure how tools that exist will handle such loads of data.

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Hi , ATpoint! Im sorry i was not clear about this. There are 796 ATACseq samples from different cancers and I want to merge all samples from a specific cancer with each other, for example I will merge 141 breast cancer bigwigs with each other. after that I will use mean signal intensity for my project

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