Bismark Genome Preparation

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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 Genome Preparation, import your data in Fasta 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 tar and gzip compressed file, genome.tgz, or directory genome which contains reference genome sequences in Fasta from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters w