HTSeq

Overview

HTSeq provides infrastructure to process data from high-throughput sequencing assays.

Version 0.9.1 is installed on the CSF. This uses Anaconda Python v4.2.0 which provides Python 3.5.2.

Restrictions on use

There are no restrictions on accessing HTSeq on the CSF. The source is released under the GNU GPL v3 license.

Set up procedure

To access the software you must first load the modulefile:

module load apps/gcc/python-packages/anaconda3-4.2.0/htseq/0.9.0

The modulefile will automatically load the required version of Anaconda modulefile for you.

Running the application

Please do not run HTSeq on the login node. Jobs should be submitted to the compute nodes via batch.

Provided also are the binaries

htseq-count

and

htseq-qa

. You can also use it within a python script with import HTSeq.

Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

python myscript.py

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• HTSeq python docs
• HTSeq website

Updates

None.