BEDTOOLS BAMtoFastq-2.26

Converts a BAM file to a fastq file

Quick Start

To use BEDTOOLS BAMtoFastq-2.26, import your data in BAM format.
Resources: https://github.com/arq5x/bedtools2

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Bedtools > BAMtoFastq

Input File(s)

Use TrmPr1_frag_1.fastq.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 names for the output fastq files (it's from a paired mapping) to bamfilep1.fastq and bamfilep2.fastq.

Default parameters only, no further configuration needed.

Output File(s)

Expect a fastq files named as set in the output.

Tool Source for App

https://github.com/arq5x/bedtools2