Calculate library complexity for Chip sep data
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5 months ago
munaj86 ▴ 20

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,,

ChIP-Seq • 245 views
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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

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5 months ago

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

Hope it helps!

Jordi

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