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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Bismark Genome Preparation

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Quick Start

Test Data

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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 -> bismark (or Community Data -> iplantcollaborative -> example_data -> bismark.20151015 for older version 0.13.1)

Input File(s)

Use tar and gzip compressed file, genome.tgz, or directory genome which contains reference genome sequences in Fasta 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:
    • Check "Compress the output into tgz file"

Output File(s)

Expect directory bismark_genome_preparation_output_bt2.tgz as output.

Tool Source for App

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