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Bam to Counts (general)


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

App Creator

Roger Barthelson

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


  • 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