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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Annotate transcripts

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This App will add existing reference annotation information to newly assembled transcripts in GFF format.

Quick Start

  • To use Annotate transcripts, import your data in GFF format. This App is part of the Alternative RNA-Seq Pipeline
  • Resources: Not available yet!

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> annotate_transcripts.

Input File(s)

Use annotation.gff and input_Athalgmap.gff and genome.fa 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.

The annotation.gff file is the input for annotation input panel. The input_Athalgmap.gff file is the input for the transcript input panel. Use genome.fa as the reference fasta input for generating a renamed transcript fasta output.

For settings for the annotation input panel use transcript_id and gene_id, then select ID for the transcript GFF tag in the transcript input panel, use the default fraction in the settings panel, select "make fasta...", input genome.fa as the reference, and select exon_id as the fasta name tag.

The GFF output should be similar to "annotated_transcripts.gff", and the fasta output should be like annotated_transcripts.gff.fa".

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