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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Samtools 1.7 bamtofastq

Converts a BAM file to a fastq file

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 -> samtools_bamtofastq

Input File(s)

Use ex1.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.

Set the name for the output fastq file.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect a fastq files named as set in the output field. 

Tool Source for App

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