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
Value
A list of quality trimmed ShortReadQ objects
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'