rep_rsem: Continuous execution of sequence alignment using RSEM
In shkonishi/rskoseq: This is my personal package of R functions for NGS data

Description

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

`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"
`prefix_fq`	character: The default value is 'sub(suffix_fq,"", list.files(fqdir))'
`...`	additional rsem-calcurate-expression options. E.g. "–fragment-length-max"

## Not run: 
# create 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/res_single_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"
fqd <- "~/pub/sampledata/rnaseq/project1/fastq"
idx <- "~/db/index/rsem_idx/cge25207.add"
unlink(alnd, recursive = T)
rskoseq::rep_rsem(alndir=alnd, idx_name=idx, fqdir = fqd, suffix_fq = "_R1.fastq.gz")

# paired
alnd <- "~/pub/sampledata/rnaseq/project1/res_paired_rsm"
fqd <- "~/pub/sampledata/rnaseq/project1/paired_fastq"
idx <- "~/db/index/rsem_idx/cge25207.add"
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)


## End(Not run)