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!
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.
Thank you! How would I create a standard count matrix to carry out the DESeq2 size factors? using featureCounts?
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.
Thank you! How would I create a standard count matrix as described? using featureCounts?
Yes, feature counts should work fine, or csaw.