Question: Normalizing Bigwig values
0
gravatar for hkitano
7 weeks ago by
hkitano0
hkitano0 wrote:

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!

bigwig bam ngs normalization • 190 views
ADD COMMENTlink modified 7 weeks ago by jared.andrews077.1k • written 7 weeks ago by hkitano0

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.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by rpolicastro1.7k

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

ADD REPLYlink written 7 weeks ago by hkitano0
1
gravatar for jared.andrews07
7 weeks ago by
jared.andrews077.1k
Memphis, TN
jared.andrews077.1k wrote:

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.

ADD COMMENTlink written 7 weeks ago by jared.andrews077.1k

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

ADD REPLYlink written 7 weeks ago by hkitano0

Yes, feature counts should work fine, or csaw.

ADD REPLYlink written 7 weeks ago by jared.andrews077.1k
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