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.
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
How about ChIPQC package in R? It has an extensive vignette.
Hope it helps!
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