rep_rsem: Continuous execution of sequence alignment using RSEM

Description Usage Arguments Examples

View source: R/rep_rsem.R

Description

Description

Usage

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

Arguments

alndir

character: output 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"

...

additional rsem-calcurate-expression options. E.g. "–fragment-length-max"

Examples

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### rep rsem
# # index ----
# rsem-prepare-reference --bowtie2 ref.fasta refname
# rsem-prepare-reference --bowtie2 --transcript-to-gene-map list.txt ref.fasta refname

# # single ----
# idx <- "~/db/index/rsem_idx/cge25207.add"
# alnd <- "~/pub/sampledata/rnaseq/project1/test_rsm"
# unlink(alnd, recursive = T)
# rskoseq::project_rnsq("~/pub/sampledata/rnaseq/project1", "res_single_rsm", "rsem")
# rskoseq::rep_rsem(alndir=alnd, idx_name=idx)
#
# # single (no project -> you must specifie fastq directory) ----
# alnd <- "~/pub/sampledata/rnaseq/res_rsm"
# unlink(alnd, recursive = T)
# fqd <- "~/pub/sampledata/rnaseq/project1/fastq"
# rskoseq::rep_rsem(alndir=alnd, idx_name=idx, fqdir = fqd)
#
# paired ----
# alnd <- "~/pub/sampledata/rnaseq/project1/test2.rsm"
# fqd <- "~/pub/sampledata/rnaseq/project1/paired_fastq"
# unlink(alnd, recursive = T)
# rskoseq::project_rnsq("~/pub/sampledata/rnaseq/project1", "res_paired_rsm", "rsem")
# rskoseq::rep_rsem(alndir = alnd, fqdir = fqd, paired = T, idx_name = idx)

shkonishi/rskoseq documentation built on Oct. 30, 2018, 1:10 p.m.