RunTrimgalore: RunTrimgalore RunTrimgalore(fileR1)

In elmerfer/Aligners:

RunTrimgalore RunTrimgalore(fileR1)

Description

RunTrimgalores is intended to perform adapters and trimming of read from paired end sequencing data

Usage

## Not run: 
file1 <- "my.file_1.fastq #it is expected to have their pair as ny.file_2.fastq
res <- RunTrimgalore(file1)
res ##this will hold the file1 name and the elapsed time as well as the file sizes prior and after trimming

## End(Not run)

Arguments

fileR1	the fastq file read 1 (the read 2 will be automatically called) accepted files are XXX_1.fastq/_r1.fastq or fq.gz. Their paired files should replace the _1 (_R1) by _2 (_R2)
replace	(boolean) If TRUE the original files will be reomved and replaced by the trimmed ones under the same original name but gziped (.fq.gz), otherwise it will created two new files as XXX_1_val_1.fq.gz and XXX_2_val_2,fq.gz

elmerfer/Aligners documentation built on May 27, 2023, 5:05 a.m.