The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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RSEM 1.2.12

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RSEM is an app for counting the number of hits for each gene or transcript in a BAM file from a read to transcript mapping.

Quick Start

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under _Community Data -> iplantcollaborative -> example_data -> _RSEM/


Input File(s)

Use BAdehydxtrinity.sorted.6747.bam and Trinity.fasta from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters , except check the box for paired reads.

Output File(s)

Expect 2 files as output, RSEM.genes.results and RSEM.isoforms.results.

Tool Source for App

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