fqfilter: Filtering and trimming of fastq files using ShortRead package
In shkonishi/rskoseq: This is my personal package of R functions for NGS data

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

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

`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

## 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)