STARalign: Align fastq.gz files with STARlong

In noush-joglekar/scisorseqr: Processes long reads for differential isoform analysis

Align fastq.gz files with STARlong

Description

This function is a wrapper for STARlong with stringent parameters optimized for PacBio sequenced data. It performs sam to bam conversion to reduce space, and .bam output is necessary for downstream analysis

Usage

STARalign('FastqFiles/','~/STARlong','~/starIndex_gencode10_sequins/',32)

Arguments

fqFolder	fastq.gz files from a single sample or replicate, or barcoded output
starProgPath	path to STARlong aligner
refGenomeIndex	location of STAR reference genome index.
numThreads	number of parallel threads to use, Defaults to 8

Value

STARoutput Folder containing star output files and reports

See Also

MapAndFilter

noush-joglekar/scisorseqr documentation built on March 18, 2023, 8:06 p.m.