Description Usage Arguments Examples
View source: R/rep_stringtie.R
Consecutive processiong of stringtie for multiple samples, then FPKM and cov data table are created. Execution following from 'rskoseq::project_rnsq', 'rskoseq::rep_hisat2'.
1 | rep_stringtie(bamdir, suffix_bam, guide_gff, res_dir, ...)
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bamdir |
character: the name of alignment directory, sorted-bam files searched from under this directory. If designate your own sorted-bam containing directory, give the path of the directory and 'res_dir' must be directory name under the 'bamdir'. |
suffix_bam |
character: The default is ".sort.bam". |
guide_gff |
The file path of guide gff. |
res_dir |
output directory path, the default is 'paste0(dirname(bamdir), "/res_stringtie")' |
... |
additional options of stringtie. E.g. "-e" |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ## Not run:
# create project directory
alnd <- "~/pub/sampledata/rnaseq/project1/test1.h2"
idx <- "~/db/index/hisat2_idx/CriGri_1.0.ens.add"
unlink(alnd, recursive = T)
rskoseq::project_rnsq("~/pub/sampledata/rnaseq/project1", "test1.h2", "hisat2")
system(paste("tree", alnd))
# run rep_hisat2
rskoseq::rep_hisat2(alndir = alnd, idx = idx, paired = F)
system(paste("tree", alnd))
# run rep_stringtie
bamdir <- "~/pub/sampledata/rnaseq/project1/test1.h2/res_hisat2"
guide <- "~/db/index/hisat2_idx/CriGri_1.0.ens.add.gff"
rskoseq::rep_stringtie(bamdir = bamdir, guide_gff = guide)
system(paste("tree", alnd))
## End(Not run)
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