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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Community rating: ?????

An HTProcess app. Takes HTProcess_BAM directory and creates counts of each component of a reference sequence 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 -> HTProcess_BAMstats

Input File(s)

Use HTProcess_BAM_control 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:
    • column naming - BAM file name
    • single file counting method - Group all single read files

Output File(s)

Expect a text file named BAM_counts.tsv as output. 

Tool Source for App

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