Bismark Methylation Extractor
Bismark Methylation Extractor
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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 Methylation Extractor, import your data in SAM 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 bismark_output_bt2.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.
- Use these parameters within the DE app interface:
- Check "single end" in "Reads type" in Parameters panel
- Check "Merge strand-specific info into context-dependent output files"
Output File(s)
Expect bismark_methylation_extractor_output.CpG.txt, bismark_methylation_extractor_output.CHG.txt, and bismark_methylation_extractor_output.CHH.txt as output.