Description Usage Arguments Examples
Create Project directories for RNA-seq pipeline using hisat2-stringtie. Then fastq files move to './project/fastq' directory, followning execution of 'rskoseq::rep_hisat2' or 'rskoseq::rep_rsem', for read mapping.
1 | project_rnsq(prjd, alnd, algnr)
|
prjd |
character: path of a project directory name |
alnd |
character: path of a alignment directory name, the default is "alignment1" |
algnr |
character: select an alignment program from "hisat2"(default), "rsem", "others" |
1 2 3 4 5 6 7 8 9 10 11 | ## Not run:
# create new project
prj <- "~/pub/sampledata/rnaseq/project1"
project_rnsq(prjd = prj, alnd = "test.h2", algnr = "hisat2")
project_rnsq(prjd = prj, alnd = "test.rsm", algnr = "rsem")
# now there is a project directory, create another alignment directory.
system(paste("tree", prj))
## End(Not run)
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