detectRRNA: Detect rRNA Contamination in Reads
Description
Returns a named vector indicating if a read ID has rRNA contamination or notUsage
detectRRNA(max_mismatches, rRNADb, options, shortread1, shortread2,
remove_tmp_dir=TRUE)Arguments
max_mismatches
Maximum number of mismatches to allow when aligning
rRNADb
the rRNA database name to search against
options
an "options" list from the HTSeqGenieBase package
shortread1
a ShortReadQ object of reads (for paired end, the first pair)
shortread2
only used with paired-end data. a ShortReadQ object of reads for the second pair
remove_tmp_dir
boolean indicating whether or not to delete temp directory of gsnap results
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