Description Usage Arguments Examples
Description
1 | rep_rsem (alndir, fqdir, paired, idx_name, suffix_fq, prefix_fq, ...)
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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" |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ## 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)
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