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docs:_DE_archived_apps_blurb
docs:_DE_archived_apps_blurb

Bismark

Community rating: ?????

Quick Start

Test Data

Info

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bismark.

Input File(s)

Ustest_reads_bs.fq as single-end fastq and bismark_genome_preparation_output as prepared genome sequence directory 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: 
    • Enter 25 in "Read length" in Parameters panel
    • Select "Phred quality plus 64" in "Quality score type" in Parameters panel

Output File(s)

Expect bismark_output.sam and bismark_output.txt as output.

Tool Source for App

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