AlignmentSTAR: Use the STAR tool to align the reads

Description Usage Arguments Details

View source: R/RNASeqPipelineR.R

Description

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

Usage

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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.