rep_stringtie: Consecutive execution of Transcript assembly and...

In shkonishi/rskoseq: This is my personal package of R functions for NGS data

Description

Consecutive processiong of stringtie for multiple samples, then FPKM and cov data table are created. Execution following from 'rskoseq::project_rnsq', 'rskoseq::rep_hisat2'.

Usage

rep_stringtie(bamdir, suffix_bam, guide_gff, res_dir, ...)

Arguments

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"

Examples

## 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)

shkonishi/rskoseq documentation built on April 18, 2021, 3:50 p.m.