HTSeq

Description

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HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

See the HTSeq documentation chapter A tour through HTSeq first for an overview on the kind of analysis you can do with HTSeq and the design of the package, and then look at the reference documentation.

While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge. See the Scripts section in the overview below for what is available.

Available versions

• 0.5.3p3 (both EL5 and EL6).

Note: HTSeq has been installed into and its module loads python/2.6.5 on EL5 and python/2.7.3 on EL6. In addition, matplotlib has been installed for htseq-qa to work.

Running the application using modules

To use htseq with the environment modules system at HPC the following commands are available:

Get module information for htseq:

$module spider htseq

Load the default application module:

$module load htseq

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_HTSEQ_DIR - directory where htseq is located.
• HPC_HTSEQ_BIN - executable directory.

How To Run

Two programs are available - htseq-count and htseq-qa. Run them without any arguments to see the usage information. The main HTSeq module can be loaded from python (import HTSeq). See HTSeq documentation for a tutorial.