Galaxy | Tool Preview

Align reads and estimate abundance (version 2.15.1+galaxy0)
de novo assembly of RNA-Seq data
Bowtie -X parameter
Additional Options
Additional Options 0

Trinity assembles transcript sequences from Illumina RNA-Seq data. This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample.


It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample. You have to choose between several counting methods.

If you dont align on a Trinity assembly, you need to provide a file of the following (tabular) format to map gene ids to transcript ids:

gene1 transcript1
gene2 transcript2


This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page: