When do the PCR Bottlenecking Coefficient

Question

[michelafrancesconi9]

Hello, I can't figure out if the PCR Bottlenecking Coefficient, needs to be done with the bam file already filtered (so I removed the duplicate values) or not filtered yet.

Thank you

[GenoMax]

PBC is described on this page: https://www.encodeproject.org/data-standards/2012-quality-metrics/

In case someone else is curious about this metric.

A measure of library complexity, i.e. how skewed the distribution of read counts per location is towards 1 read per location.

PBC = N1/Nd

(where N1= number of genomic locations to which EXACTLY one unique mapping read maps, and Nd = the number of genomic locations to which AT LEAST one unique mapping read maps, i.e. the number of non-redundant, unique mapping reads).

Provisionally, 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, while 0.9-1.0 is no bottlenecking.

[michelafrancesconi9]

Thank you but I still do not understand what kind of file I have to use