GenePattern offers a suite of tools to support a wide variety of RNA-seq analyses, including short-read mapping, identification of splice junctions, transcript and isoform detection, quantitation, and differential expression. The modules have been adapted from widely-used tools. GenePattern also provides pipelines that allow you to perform a number of multi-step RNA-seq analyses automatically.
- Alignment: Bowtie.aligner
- Differential Expression: Cufflinks.cuffdiff
- Genome Annotation: Cufflinks, Cufflinks.cuffcompare, Scripture
- Isoform Detection: Tophat
- RNA Quantitation: Cufflinks, Scripture
- Utilities: Bowtie.indexer, BamToSam, ExprToGct, SamToBam, SortSam
- Visualizers: IGV