HTSeqGenie (version 4.2.0)

isAdapter: Detect adapter contamination

Description

Does a Needleman-Wunsch like small-in-large alignment of the adapter vs each read. Flag read if score exceeds threshold

Usage

isAdapter(reads, score_cutoff, adapter_seqs)

Arguments

reads

Set of reads as ShortRead object

score_cutoff

Alignment score threshold that needs to be exceeded to be flagged as adapter. Usually this value is determined empirically by getAdpaterThreshold()

adapter_seqs

One or more adapter sequences

Value

boolean vector indicating adapter contamination