kallistoAlign: Use the Kallisto tool to align and quantify RNASeq FASTQ...

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

Description

Uses Kallisto to pseudo-align reads in FASTQ files against the reference genome transcripts. Optionally you can specify paired end reads. The code assumes paired reads have different suffixes defined by 'paired_pattern' (i.e. sampleA_read_R1.fastq, sampleA_read_R2.fastq). Read 1 is assumed to be upstream and read 2 is assumed to be downstream. FASTQ files must have the suffix 'fastq' or fq'. If running locally the number of available nodes should be at least the number of kallisto cores plus one times the number of parallel threads.

Usage

kallistoAlign(kallisto_threads = 3, paired = TRUE,
  minutes_requested = 10, slurm = TRUE, parallel_threads = 1,
  slurm_partition = NULL, force = FALSE,
  paired_pattern = c("_1.fastq", "_2.fastq"), fastqPath = "",
  mail = NULL)

Arguments

kallisto_threads	specify how many threads kallisto should use. This will be input as the '-t' parameter in the kallisto command. Default is 3 as the majority of gizmo nodes have 4 processors.
paired	specify whether you have paired reads or not.
minutes_requested	number of minutes requested for the job (when submitting a slurm job). Generally kallisto takes less than 5 minutes to complete. Scicomp recommended 10m. Ignored if slurm = FALSE
slurm	if TRUE job is submitted as a slurm batch job, otherwise it's run on the local machine. Slurm jobs will honour the nchunks and minutes_requested arguments.
parallel_threads	Number of threads to run concurrent kallisto jobs if not using SLURM. Total number of threads required are parallel_threads*(kallisto_threads+1).
slurm_partition	the slurm partition to submit to. Defaults to campus.Ignored if slurm=FALSE
force	If TRUE then align all FASTQ files else only align those files that have not been aligned. If force is FALSE then only fastq files without a directory in the Kallisto directory will be aligned.
paired_pattern	specify the suffix of the paired-end fastq file names. Each suffix must be of the same length.
fastqPath	specify path to FASTQ files if different than default (FASTQ directory)
mail	email address to send failure message to, if desired.

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