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Question: QC for broad domain chip-seq data?
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If you do narrow peak calling you can do autocorrelation as a form of QC. This is just comparing the peaks from the two-strands for the same potential peak.

I cannot think of anything similar that would work on broad domains.

Some stupid ideas for QC to get the creative juices flowing:

  • Find regions that are always eu/heterochromatic in all tissues according to the epigen roadmap and see that those respective regions contain H3K4me3/H3K27me3 respectively in the data you are analysing...
  • Investigate genes you know are supposed to be on/off in the data you have to see whether they are considered enriched for the appropriate histone modification...

Can you think of anything else?

ADD COMMENTlink 4.0 years ago Endre Bakken Stovner • 880 • updated 4.0 years ago Biostar 20
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You can still look at correlation, just don't do it with peaks (see, for example, multiBamSummary and plotCorrelation in deepTools.

ADD REPLYlink 4.0 years ago
Devon Ryan
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