Galaxy |

Align reads and estimate abundance (version 2.15.1+galaxy0)

Transcripts:

de novo assembly of RNA-Seq data

Paired or Single-end data?:

Left/Forward strand reads:

Right/Reverse strand reads:

Strand specific data:

Maximum insert size:

Bowtie -X parameter

Abundance estimation method:

Alignment method:

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.

Inputs

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

Output

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