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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, import your data in Fastq format.
- Resources: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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| Info |
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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.
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- Use these parameters within the DE app interface:
- Enter 25 in "Read length" in Parameters panel
- Select "Phred quality plus 64phred64" in "Quality score type" in Parameters panel
Output File(s)
Expect bismark_output.sam and bismark_outputbt2.txt bam as output.
Tool Source for App
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