Difference between revisions of "SpliceGrapher"
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | M. F. Rogers, J. Thomas, A. S. N. Reddy, A. Ben-Hur. SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data. Genome Biology, Vol. 13, 2012. | + | * M. F. Rogers, J. Thomas, A. S. N. Reddy, A. Ben-Hur. SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data. Genome Biology, Vol. 13, 2012. |
| − | M. F. Rogers, C. Boucher, A. Ben-Hur. SpliceGrapherXT: from splice graphs to transcripts using RNA-Seq. ACM-BCB 2013 | + | * M. F. Rogers, C. Boucher, A. Ben-Hur. SpliceGrapherXT: from splice graphs to transcripts using RNA-Seq. ACM-BCB 2013 |
|}} | |}} | ||
Latest revision as of 21:24, 6 December 2019
Description
SpliceGrapher is a Python package for creating splice graphs from RNA-Seq data, guided by gene models and EST data (when available). Starting with version 0.2.2 we introduced SpliceGrapherXT that can convert splice graph predictions into transcript predictions.
Environment Modules
Run module spider splicegrapher to find out what environment modules are available for this application.
System Variables
- HPC_SPLICEGRAPHER_DIR - installation directory
- HPC_SPLICEGRAPHER_BIN - executable directory
Citation
If you publish research that uses splicegrapher you have to cite it as follows:
- M. F. Rogers, J. Thomas, A. S. N. Reddy, A. Ben-Hur. SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data. Genome Biology, Vol. 13, 2012.
- M. F. Rogers, C. Boucher, A. Ben-Hur. SpliceGrapherXT: from splice graphs to transcripts using RNA-Seq. ACM-BCB 2013