detectRRNA: Detect rRNA Contamination in Reads

Description Usage Arguments Details Value Author(s)

Description

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

Usage

1
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

Details

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

Value

a named logical vector indicating if a read has rRNA contamination

Author(s)

Cory Barr


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