Description Usage Arguments Examples
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 |
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)
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