SpliceGrapher¶
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.
Environment Variables¶
- HPC_SPLICEGRAPHER_DIR - installation directory
- HPC_SPLICEGRAPHER_BIN - executable directory
Citation¶
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
Categories¶
biology, sequencing