RNASeqGenie (version 1.0.44)

detectAdapterContam: Detect Adapter Contamination in Reads

Description

Detect Adapter Contamination in Reads

Usage

detectAdapterContam(reads, score_cutoff, paired_ends,
    force_paired_end_adapter, pair_num=1)

Arguments

reads

A ShortReadQ or DNAStringSet of reads to check for adapter contamination

score_cutoff

The alignment score cutoff to consider adapter contaminated

paired_ends

boolean indicating if reads are paired end

force_paired_end_adapter

diagnostic tool. Not for end users.

pair_num

Which end of the read pairs the sequence is from

Value

• a boolean