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SW:Qualimap

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Qualimap

GCATemplates available: no

Qualimap homepage

  • fast analysis across the reference genome of mapping coverage and nucleotide distribution;
  • easy-to-interpret summary of the main properties of the alignment data;
  • analysis of the reads mapped inside/outside of the regions defined in an annotation reference;
  • computation and analysis of read counts obtained from intersting of read alignments with genomic features;
  • analysis of the adequacy of the sequencing depth in RNA-seq experiments;
  • support for multi-sample comparison for alignment data and counts data;
  • clustering of epigenomic profiles.
module spider Qualimap

Enter the following command to see the command line options

qualimap -h

Qualimap will use more than one core so you will need to specify the number of cores using the qualimap -nt option.

You can capture the number of cores you specify in the Slurm parameters with the environment variable $SLURM_CPUS_PER_TASK

For example if you have these Slurm parameters:

#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=28

Then you can use the -n value with the environment variable $SLURM_CPUS_PER_TASK to specify the number of cores for qualimap to use

qualimap -nt $SLURM_CPUS_PER_TASK

If you run qualimap without options, it will start the GUI version. The GUI version works best with the HPRC Portal.

If you would like to use the GUI version, you can login to the OnDemand portal at portal.hprc.tamu.edu and select VNC in the 'Interactive Apps' tab. You might start with all cores and all memory initially until you get an idea of how much memory is required for Qualimap.

When the VNC loads after clicking the blue launch button, you will reach a terminal where you can start the GUI version of Qualimap with the following commands

module purge
module spider Qualimap
# load the latest version using the appropriate module load command then run qualimap
qualimap