The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq datasets.

References:

• Hartley, S. W. & Mullikin, J. C. 2015. QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments BMC Bioinformatics 16:224.

• QoRTs Project Page
• QoRTs GitHub Page

• Module Name: QoRTs (see the modules page for more information)
• Multithreaded
• Environment variables set
  • QORTS_JAR -- filepath for the essential QoRTs.jar jarfile
  • QORTS_JARPATH -- generic path to jar files
  • QORTS_EXAMPLES -- full example file set

QoRTs is a mixture of java and R. The jarfile can be executed directly using the $QORTS_JARFILE environment variable:

java -Xmx1G -jar $QORTS_JARFILE --man

NOTE: Memory and scratch space are handled through java options -Xm and -Djava.io.tmpdir. The amount of memory needed is 10-20GB for most genomes. To allocate 10GB of RAM to the java machine, include the option -Xmx10G.

The R steps are done as with any R job:

R
> library(QoRTS);

There is an example walkthrough available which uses data available in $QORTS_EXAMPLES.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=16 --mem=10g --gres=lscratch:100
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load QoRTs
[user@cn3144 ~]$ cp -R $QORTS_EXAMPLES/* .
[user@cn3144 ~]$ sh exampleScripts/step0/step0.reset.sh
[user@cn3144 ~]$ mkdir -p outputData/qortsQcData/SAMP1_RG1
[user@cn3144 ~]$ java -Xmx10G -jar -Djava.io.tmpdir=/lscratch/$SLURM_JOB_ID \
 $QORTS_JARFILE QC --stranded inputData/bamFiles/SAMP1_RG1.bam \
 inputData/annoFiles/anno.gtf.gz outputData/qortsQcData/SAMP1_RG1/

[user@cn3144 ~]$ while read line
do
  mkdir outputData/qortsData/$line/
  java -Xmx10G -Djava.io.tmpdir=/lscratch/$SLURM_JOB_ID \
    -jar $QORTS_JARFILE QC --stranded \
    inputData/bamFiles/$line.bam \
    inputData/annoFiles/anno.gtf.gz \
    outputData/qortsData/$line/
done < "inputData/annoFiles/uniqueID.list.txt"

[user@cn3144 ~]$ R
library(QoRTs):
res <- read.qc.results.data("outputData/qortsData/",
  decoder.files = "inputData/annoFiles/decoder.byUID.txt",
  calc.DESeq2 = TRUE,
  calc.edgeR = TRUE);
makeMultiPlot.all(res,
  outfile.dir = "outputData/qortsPlots/summaryPlots/",
  plot.device.name = "png");

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. QoRTs.sh). For example:

#!/bin/bash
module load QoRTs

java -Xmx10G \
  -Djava.io.tmpdir=/lscratch/$SLURM_JOB_ID \
  -jar $QORTS_JARFILE QC \
  --stranded \
  --chromSizes inputData/annoFiles/chrom.sizes \
  --trackTitlePrefix SAMP1_RG1_WIGGLE  \
  inputData/bamFiles/SAMP1_RG1.bam \
  inputData/annoFiles/anno.gtf.gz \
  outputData/qortsQcData/SAMP1_RG1/

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=10g --gres=lscratch:100 QoRTs.sh