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How to convert normalized BigWig file to count matrix?

Hi,

I have some normalized BigWig files and now I want to convert these normalized BigWig files to count matrix. Can anyone give me any advice? I will appreciate it if you could give me some advice.

Thanks in advance!

count-matrix bigwig
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written by feather-W • feather-W

I want to use the matrix derived from bigwig files to perform different analysis by DESeq2 or edgeR.

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written by feather-W • feather-W

bigwig is chrom/start/end/value . what kind of matrix do you want ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre,

Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file has been normalized.

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written by feather-W • feather-W

1 answer

It's not possible. Gene counts are a region aggregate, bigwigs are a per-base readout and you cannot use normalized counts for mentioned tools.

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written by ATpoint ATpoint

Hi ATpoint,

Thanks for your reply!

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written by feather-W • feather-W

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