HTSeqGenie (version 4.2.0)

detectRRNA: Detect rRNA Contamination in Reads

Description

Returns a named vector indicating if a read ID has rRNA contamination or not

Usage

detectRRNA(lreads, remove_tmp_dir = TRUE, save_dir = NULL)

Arguments

lreads

A list of ShortReadQ objects

remove_tmp_dir

boolean indicating whether or not to delete temp directory of gsnap results

save_dir

Save directory

Value

a named logical vector indicating if a read has rRNA contamination

Details

Given a genome and fastq data, each read in the fastq data is aligned against the rRNA sequences for that genome