fqfilter: Filtering and trimming of fastq files using ShortRead package

Description Usage Arguments Examples

View source: R/fqfilter.R

Description

filtering and trimming of fastq files and output filtered and compressed fastq files

Usage

1
fqfilter (fqd, sffx, outd, qs, nhead, ntail, droplen)

Arguments

fqd

character: the fully path of a directory of fastq files, or the path of fastq files.

sffx

character: suffix of fastq files. The default value is ".fastq.gz"

outd

output directory

qs

ASCII character corresponding to q-score.

nhead

integer: Remove leading nucleotides.

ntail

integer: Remove trailing nucleotides.

droplen

integer: drop length

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
## Not run: 
# output filterd and compressed fastq files ##
fqd <- system.file("extdata/E-MTAB-1147", package = "ShortRead")
sffx <- ".fastq.gz"
outd <- "~/pub/sampledata/rnaseq/project1/qcfq"
unlink(outd, recursive = T)
fqfilter(fqd=fqd, outd=outd, droplen = 30)

# filtered fastq
qcfq <- list.files(outd, "qc.fastq.gz", full.names =T)

## End(Not run)

shkonishi/rskoseq documentation built on April 18, 2021, 3:50 p.m.