Difference between revisions of "HTSeq"
Moskalenko (talk | contribs) m (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==") |
Moskalenko (talk | contribs) |
||
| Line 38: | Line 38: | ||
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. | 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. | ||
| − | + | <!--Modules--> | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | <!-- --> | ||
{{#if: {{#var: mod}}|==Execution Environment and Modules== | {{#if: {{#var: mod}}|==Execution Environment and Modules== | ||
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
Revision as of 02:48, 10 August 2012
Description
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.
Execution Environment and 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.