AlignmentSTAR: Use the STAR tool to align the reads

In RGLab/RNASeqPipelineR: Construct Standardized pipelines for processing RNASeq data

Description

Use the STAR tool to align reads and generate transcriptome bam files

Usage

AlignmentSTAR(parallel_threads = 1, star_threads = 1, SJ_num = 5e+06,
  paired = TRUE, force = FALSE, paired_pattern = c("_1.fastq",
  "_2.fastq"), fastqPath = "")

Arguments

parallel_threads	specify how many parallel processes to spawn
star_threads	specify how many threads star should use.
SJ_num	argument for STAR parameter 'limitOutSJcollapsed' which is number of collapsed splice junctions allowed. Must be integer > 0
paired	specify whether you have paried reads or not.
force	force STAR to align all FASTQ files
paired_pattern	specify the suffix of the paired-end fastq file names. If not paired then use only a single suffix.
fastqPath	specify path to FASTQ files if different than default

Details

Uses STAR to align reads in FASTQ files against the reference genome. Optionally you can specify paired end reads. The code assumes paired reads have fastq files that differ by one character (i.e. sampleA_read1.fastq, sampleA_read2.fastq) and will perform matching of paired fastq files based on that assumption using string edit distance. Read 1 is assumed to be upstream and read 2 is assumed to be downstream. The number of parallel_threads*star_threads should not be more than the number of cores available on your system.

RGLab/RNASeqPipelineR documentation built on Jan. 19, 2020, 12:31 a.m.