trim.gal: trim.gal

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run Trim Galore

Usage

trim.gal(fq1, fq2, trim.quality=30, trim.clip_R1=13, trim.clip_R2=13, output.dir, run.cmd=TRUE, mc.cores=1)

Arguments

fq1	Path to read1 fastq files
fq2	Path to read2 fastq files
output.dir	Output directory
trim.quality	A parameter value for –quality in trimgalore. A numeric value of phred score cutoff to trim (default=30)
trim.clip_R1	A parameter value for –clip_R1 in trimgalore. A numeric value of bp to remove adaptor from the 5-prime end of read1 files (default=13)
trim.clip_R2	A parameter value for –clip_R2 in trimgalore. A numeric value of bp to remove adaptor from the 5-prime end of read2 files (default=13)
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.

Details

Trims low quality bases, and cleans up adapter sequences for paired-end files.

Value

Trimmed fastq files (e.g., .val_1.fastq, .val_1.fastq)

References

Krueger F. Trim Galore!

See Also

https://www.bioinformatics.babraham.ac.uk/projects/trim_galore

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.