Calculate library complexity for Chip sep data

Question

[munaj86]

Hi,,

I want to calculate the library complexity of my chips data using the NRF (non-redundant fraction) and PCR Bottlenecking Coefficient 1 (PBC1), is anyone can share the command in linux to get the output for these two parameters.

Thanks,,

[Friederike]

I am not aware of any library that does it, but it seems to be part of some pipelines, e.g. https://github.com/ENCODE-DCC/chip-seq-pipeline The "fingerprint" implemented in deepTools may already give you a good idea of the quality, too: https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html

Answer 1

[jordi.planells]

How about ChIPQC package in R? It has an extensive vignette.

Hope it helps!

Jordi