Bismark Genome Preparation
Bismark Genome Preparation
Community rating: ?????
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 with the above input file(s) to get the output provided in the next section below.
- Use these parameters within the DE app interface:
- Check "Compress the output into tgz file"
Output File(s)
Expect directory bismark_genome_preparation_output_bt2.tgz as output.