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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Description and Quick Start

Prepares transcripts from genome files and matching GTF files. 

Test Data:
 Community Data > iplantcollaborative > example_data > RSEM_prepare_reference > input
 Input Files -- 2 files needed. A genome sequence file, and a matching .gtf annotation or assembly file. The test files are genome.fas and annotation.gtf

Parameters Used in App: No special parameters or options. 

Output Files: A series of files is created. The main one of interest is the transcript sequence file. Others list the chromosomes or scaffolds in an assembly, and other intermediate files.
Test output files:     Community Data > iplantcollaborative > example_data > output > RSEM_prepare_referenceArabidopsis.transcripts.fa


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