raid_split_reads: Split reads from FASTQ files

In jessievb/RAID: Split barcoded FASTQ files and analyse data from the iSeq method

Description

First, the iseq_split_reads function uses shortread package function "readFastq" to load all reads from a .fastq or .fastq.gz file. Then the reads containing an anchor sequence are extracted and these reads are split to retreive - UMI - Barcode_1 sequences (and stored in a table with 2 columns) Finally a column with the sample_ID is added.

Usage

raid_split_reads(fastq_file)

Arguments

fastq_file

fastq formatted files in a directory path. Default settings or more information from ShortRead::readFastq(fastq_file)

Value

a tsv file with three columns: UMI , Barcode_1 , sample_ID

See Also

ShortRead::readFastq

Examples

RAID_split_reads("experiment/data/sample-ID.fastq.gz")

jessievb/RAID documentation built on May 16, 2019, 11:08 a.m.