PBC: PCR bottleneck coefficient

In imbforge/encodeChIPqc: A set of useful ChIPseq QC metrics from the ENCODE project

Description

Calculate the PCR bottleneck coefficient as described in the ENCODE guidelines.

Usage

PBC(IP)

Arguments

The	path to the .bam file of a ChIP sample or a GAlignments object of the ChIP sample.

Details

The PCR bottleneck coefficient (PBC) is a measure of library complexity, i.e. how skewed the distribution of read counts per location is towards 1 read per location.

Defined in the ENCODE guidelines (https://genome.ucsc.edu/ENCODE/qualityMetrics.html) as:

PBC = N1/Nd

with

• N1: Number of genomic locations to which EXACTLY one unique mapping read maps.

• Nd: Number of genomic locations to which AT LEAST one unique mapping read maps, i.e. the number of non-redundant, unique mapping reads.

PBC is further described on the ENCODE Software Tools page. 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. Very low values can indicate a technical problem, such as PCR bias, or a biological finding, such as a very rare genomic feature. Nuclease-based assays (DNase, MNase) detecting features with base-pair resolution (transcription factor footprints, positioned nucleosomes) are expected to recover the same read multiple times, resulting in a lower PBC score for these assays. Note that the most complex library, random DNA, would approach 1.0, thus the very highest values can indicate technical problems with libraries. It is the practice for some labs outside of ENCODE to remove redundant reads; after this has been done, the value for this metric is 1.0, and this metric is not meaningful. 82% of TF ChIP, 89% of His ChIP, 77% of DNase, 98% of FAIRE, and 97% of control ENCODE datasets have no or mild bottlenecking.

Value

The PBC coefficient.

Examples

pbc <- PBC("IP.bam")

imbforge/encodeChIPqc documentation built on May 18, 2019, 4:45 a.m.