generateAlignBam: Align the sequence to the reference genome with STAR

In BMILAB/scAPAtrap: Identification and Quantification of Alternative Polyadenylation Sites from Single-cell RNA-seq Data

Align the sequence to the reference genome with STAR

Description

Align the sequence to the reference genome with STAR

Usage

generateAlignBam(star.path, indexdir, input.seq, prefix, thread = 12, ...)

Arguments

star.path	The path of the STAR.
indexdir	Directory of reference genome index.
input.seq	Input fastq file.
prefix	The prefix of the output file name.
thread	Number of CPU threads, default is 12.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If 'TRUE' basic status updates will be printed along the way. logf If not NULL, then it should be a character string denoting a file name. Then message will be written to 'logf'. notRun Default is FALSE. If 'TRUE', the Shell commands inside this function will not run but output the commad line.

Examples

star.path='/home/dell/miniconda3/envs/scAPA/bin/STAR'
indexdir <- "./"
input.seq <- 'SRR1610598_2.extracted.fastq'
## Not run: 
generateAlignBam(star.path, indexdir, input.seq, prefix='./BAM/rep1',12)

## End(Not run)
generateAlignBam(star.path, indexdir, input.seq, prefix='./BAM/rep1', notRun=TRUE)

BMILAB/scAPAtrap documentation built on Oct. 13, 2023, 2:36 a.m.