Normalizing Bigwig values

Question

[hkitano]

What is the best method to normalize the values in a bigwig or bedGraph file? I am trying to compare two bigwig files, one whose range is between 0 and approximately 0.01, and another that is between 0 and 800. Thank you!

[rpolicastro]

The bamCompare function from deepTools will allow the creation of a library size normalized bigwig comparing two samples.

If you want a normalized bigwig per sample, consider using the library size factors from DESeq2 or EdgeR when making individual bigwigs with deepTools, using them as input in the --sizeFactor argument.

[hkitano]

Thank you! How would I create a standard count matrix to carry out the DESeq2 size factors? using featureCounts?

Answer 1

[jared.andrews07]

There is a very good answer by ATpoint that gets into this and how to use the size factors from DESeq2 or edgeR to normalize bigwigs as rpolicastro mentions.

[hkitano]

Thank you! How would I create a standard count matrix as described? using featureCounts?

[jared.andrews07]

Yes, feature counts should work fine, or csaw.