rep_rsem: Continuous execution of sequence alignment using RSEM

Description Usage Arguments Examples

View source: R/rep_rsem.R

Description

Description

Usage

1
rep_rsem (alndir, fqdir, paired, idx_name, suffix_fq)

Arguments

alndir

alignment directory path, created by rskoseq::project_rnsq.

fqdir

character: the fully path of fastq files. The default is 'paste0(dirname(alndir), "/fastq")'. If this directory containing still analyzed fastq and additional fastq files,

paired

logical: paired or single read. If paired end, the names of fastq file must be "_R1" and "_R2".

idx_name

rsem index file path

suffix_fq

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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
##
### rep rsem
# single ----
# idx <- "~/db/index/rsem_idx/cge25207.add"
# alnd <- "~/pub/sampledata/rnaseq/project1/test.rsm"
# unlink(alnd)
# rskoseq::project_rnsq("~/pub/sampledata/rnaseq/project1", "test.rsm", "rsem")
# rskoseq::rep_rsem(alndir=alnd, idx_name=idx)

# paired ----
# alnd <- "~/pub/sampledata/rnaseq/project1/test2.rsm"
# fqd <- "~/pub/sampledata/rnaseq/project1/paired_fastq"
# unlink(alnd)
# rskoseq::project_rnsq("~/pub/sampledata/rnaseq/project1", "test2.rsm", "rsem")
# rskoseq::rep_rsem(alndir = alnd, fqdir = fqd, paired =T, idx_name = idx)

shkonishi/rskoseq documentation built on June 24, 2018, 6:19 a.m.