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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Heterozygote Bam to Counts, v1.2

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Enter a bam file and a matching annotation file and get counts for transcripts or genes

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 ->bam2countsGeneral

Input File(s)

Use hy5_rep1.bam and annotation.gff 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 and set feature to count to gene_name.

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 hy5testout.

Tool Source for App


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