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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HTSeq-count 0.5.4 

Community rating: ?????

A tool for counting the number of reads that fall within the range of features defined in a GFF file.

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 -> htseq_count.

Input File(s)

Use testfile.sam and hy5_rep1_transcripts.gtf 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.


  • Use these parameters within the DE app interface:
    • MODE - union
    • feature type - exon
    • feature attribute - gene_id
    • default for the rest

Output File(s)

Expect a tab delimited file as output. For the test case, the output file you will find in the example_data directory is named FeatureCounts.txt.


Tool Source for App

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