JETTA detects alternatively spliced exons based on pre-calculated statistics of exons and junctions in RNA-Seq data sets. It does not support low-level RNA-Seq analysis such as base calling, mapping, alignment, transcript assembly, and expression calculation. For low-level RNA-Seq analysis, please refer to SeqMap, rSeq, and SpliceMap or other tools.
Input Data Files – JETTA requires the following files
- Gene expression file. See an example.
- Exon expression file. See an example.
- Junction expression file (only for junction supports). See an example.
- Alternative splicing structure file (only for junction supports). See an example.
These expression matrixes can be calculated from any RNA-Seq platform, but Illumina RNA-Seq plaforms with GA-II, GA-IIx and HiSeq2000 are suggested. Each expression files should contain samples of two conditions, and at least more than two samples for each condition.
Availability – JETTA source codes and other downloads are available at: http://gluegrant1.stanford.edu/~junhee/JETTA/