Difference between revisions of "HTSeq"
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|{{#vardefine:app|htseq}} | |{{#vardefine:app|htseq}} | ||
|{{#vardefine:url|http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html}} | |{{#vardefine:url|http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html}} | ||
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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|{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
|{{#vardefine:faq|}} <!--Enable FAQ section --> | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| − | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | + | |{{#vardefine:citation|1}} <!--Enable Reference/Citation section --> |
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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--> | <!--Modules--> | ||
| − | + | ==Environment Modules== | |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_HTSEQ_BIN - executable directory. | * HPC_HTSEQ_BIN - executable directory. | ||
| − | {{#if: {{#var: exe}}|== | + | <!--Additional--> |
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
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. | 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. | ||
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
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{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{{app}}} you have to cite it as follows: | If you publish research that uses {{{app}}} you have to cite it as follows: | ||
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| + | Simon Anders, Paul Theodor Pyl, Wolfgang Huber | ||
| + | HTSeq — A Python framework to work with high-throughput sequencing data | ||
| + | Bioinformatics (2014), in print, online at [http://doi:10.1093/bioinformatics/btu638 doi:10.1093/bioinformatics/btu638]. | ||
|}} | |}} | ||
Latest revision as of 19:05, 12 August 2022
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.
Environment Modules
Run module spider htseq to find out what environment modules are available for this application.
System Variables
- HPC_HTSEQ_DIR - installation directory
- HPC_HTSEQ_BIN - executable directory.
Additional Information
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.
Citation
If you publish research that uses {{{app}}} you have to cite it as follows:
Simon Anders, Paul Theodor Pyl, Wolfgang Huber HTSeq — A Python framework to work with high-throughput sequencing data Bioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638.