SAMtools view-BEDtools bamtoFastq

This app uses SAMtools view to filter either mapped or unmapped reads from a BAM file. Then BEDtools bamtofastq is used to convert the remaining reads to a fastq file.

Quick Start

To use SAMtools view-BEDtools bamtoFastq import your data in BAM format.
Resources: https://github.com/arq5x/bedtools2, http://www.htslib.org/doc/samtools-1.7.html

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.

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, http://www.htslib.org/doc/samtools-1.7.html