View source: R/RNASeq_kallisto.R
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.
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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 |
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. |
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