How can I check library diversity in ChIPSeq data ?

Question

[Tori]

I have ChIP-Seq data and I would like to know if the data has low diversity library? Are there any tools for this purpose?

Answer 1

[dariober]

I would have a look at (more or less in this order):

• FastQC report for overrepresented kmers, sequences and adapter contamination
• Picard tools, particular EstimateLibraryComplexity and MarkDuplicates for duplication rate
• deepTools, bamFingerprint is quite handy to assess the level of enrichment

However, I think most of the statistics reported by these tools are meaningful if you have a prior idea of what a good library would look like. In the case of ChIP-Seq it might depend on what you are ChIP'ing.