clipFastqFile: Clip Bases from FASTQ reads

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Clip Bases from FASTQ reads

Description

Clip (trim) bases from the 5' and/or 3' ends of reads in a FASTQ file

Usage

clipFastq(filein, fileout, clip5prime = 0, clip3prime = 0)

Arguments

filein	Existing FASTQ file of reads and quality scores
fileout	New created FASTQ file with shorter reads and quality scores
clip5prime	number of bases to trim from the 5' end (high quality, front)
clip3prime	number of bases to trim from the 3' end (low quality, tail)

Details

Overwrites the new output file if it already exists. Either file may be compressed if the given file suffix ends with .gz

Value

No return value. Creates a new FASTQ file with the same number of reads.

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.