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Dear all,
Which tools would you recommend the most when performing differential binding in ChIP-seq ? Thank you,
~ Bogdan
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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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Cross-posted https://www.biostars.org/p/9524012/#9524012
https://www.biostars.org/p/9524012/#9524012 geometry dash unblocked It is very useful.