Bismark

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Quick Start

The newer version 0.14.5 uses bowtie2 instead of bowtie, so you have to rebuild index if you have index generated by older version.
To use Bismark, import your data in Fastq format.
Resources: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

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 test_reads_bs.fq as single-end fastq and bismark_genome_preparation_output_bt2.tgz as prepared genome sequence directory 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:
- Select "phred64" in "Quality score type" in Parameters panel

Output File(s)

Expect bismark_output_bt2.bam as output.

Tool Source for App

http://www.bioinformatics.babraham.ac.uk/projects/bismark/