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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IGVtools count 

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The "count" command computes average feature density over a specified window size across the genome. Common usages include computing coverage for alignment files and counting hits in Chip-seq experiments.

Quick Start

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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 from the directory above as test input.

Parameters Used in App

  • Default parameters only, no further configuration needed.

Tool Source for App

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