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An HTProcess app. Takes HTProcess_BAM directory and creates counts of each component of a reference sequence file.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> HTProcess_BAMstats
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
Expect a text file named BAM_counts.tsv as output.