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Community rating: ?????

Quick Start



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)

Ustest_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.


  • 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