trimTailsByQuality: Trim off low quality tail

In HTSeqGenie: A NGS analysis pipeline.

Description

The illuminsa manuals states: If a read ends with a segment of mostly low quality (Q15 or below), then all of the quality values in the segment are replaced with a value of 2( encoded as the letter B in Illumina's text-based encoding of quality scores)... This Q2 indicator does not predict a specific error rate, but rather indicates that a specific final portion of the read should not be used in further analyses.

Usage

trimTailsByQuality(lreads, minqual = "#")

Arguments

lreads	A list (usually a pair) of ShortReadQ object
minqual	An ascii encoded quality score

Details

For illumina 1.8 the special char is encoded as '#', which we chhose as default here. For illumina 1.5 make sure to set the minqual to 'B'

Value

A list of quality trimmed ShortReadQ objects

HTSeqGenie documentation built on Nov. 8, 2020, 6:12 p.m.