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 Methylation Extractor

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

Input File(s)

Use bismark_output_bt2.bam 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 "single end" in "Reads type" in Parameters panel
    • Check "Merge strand-specific info into context-dependent output files"

Output File(s)

Expect bismark_methylation_extractor_output.CpG.txt, bismark_methylation_extractor_output.CHG.txt, and bismark_methylation_extractor_output.CHH.txt as output.

Tool Source for App

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