performing the differential binding in ChIP-seq
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Bogdan ▴ 640
@bogdan-2367
Last seen 5 weeks ago
Palo Alto, CA, USA

Dear all,

Which tools would you recommend the most when performing differential binding in ChIP-seq ? Thank you,

~ Bogdan

ChIP-seq • 217 views
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@8f9d24cc
Last seen 3 days ago
United States

DiffBind https://bioconductor.org/packages/release/bioc/html/DiffBind.html

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Thank you. Yes, DiffBind might be a good choice shall we have replicates per sample. Another choice is MA-norm2. Any other well-tested suggestions please ?

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I am asking the question because we have two sets of ChIP-seq data for a histone mark (lets' say H3K4me1) that were generated with :

<> an antibody Ab1

<> an antibody Ab2

What is the best method to compare these two ChIP-seq datasets in order to be able to say :

Ab1 works better than Ab2 ?

We do not have replicates in order to use DiffBind.

Thanks,

Bogdan

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Without replicates, I would use normalized bigwig files in IGV and look at locations where you expect to see a peak. Using normalized bigwig files, if all the peaks you look at (I would look at 20-30) are bigger with the antibody Ab1 compared to the antibody Ab2, it will give you a good indication that your Ab1 is better than your Ab2. Obviously, it is not ideal but if you are interested in a specific set of genes, it should give your the answer you are looking for. For normalization, I would use deepTools bamCoverage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
You can try different types of normalization. I did not observe any differences between the different normalization methods (RPGC, RPKM, CPM, BPM...) when looking at the normalized bigwig files in IGV at the few chromosomal locations so I usually pick RPGC.

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