realizeReads: Realize read sequences

In MarioniLab/sarlacc: Pipeline for Oxford Nanopore RNA-Seq Data Analysis

Description

Execute delayed operations (reverse-complementing, trimming) to generate the actual read sequences.

Usage

realizeReads(aligned, number=1e5, trim=TRUE) 

Arguments

aligned	A DataFrame of alignment results produced by adaptorAlign - or, if trim=TRUE, by filterReads.
number	Integer scalar specifying the number of records to read at once from the FASTQ file, see ?FastqStreamer.
trim	Logical scalar indicating whether adaptor trimming should be performed.

Details

This function will parse the FASTQ file to extract the read sequences corresponding to the row names of aligned. It will then perform reverse-complementing according to aligned$reversed to coerce all reads into the canonical orientation, see ?adaptorAlign for details. Finally, if trim=TRUE, it will trim off the adaptor sequences on the ends of the reads.

The reverse complementing and trimming can be envisaged as delayed operations from the previous functions (adaptorAlign and filterReads, respectively). This sacrifices speed for memory efficiency in those steps, by avoiding the need to explicitly load the read sequences into memory. Here, we have assumed that the number of reads is sufficiently reduced (e.g., by filtering and demultiplexing) to be able to load all reads.

Value

A QualityScaledDNAStringSet object containing read sequences.

Author(s)

Aaron Lun

See Also

adaptorAlign and filterReads for generation of aligned.

Examples

example(filterReads)
realizeReads(filt)

MarioniLab/sarlacc documentation built on May 13, 2019, 12:51 p.m.