| TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Please cite: Trapnell, C., Pachter, L. and Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009). |
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/tophat
| Name | Version | Type | |
|---|---|---|---|
| bowtie | 0.12.7 | package | |
| samtools | 0.1.18 | package | |
| tophat | 1.4.0 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Find splice junctions using RNA-seq data | 1.5.0 | any | |