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Tallymer-occratio

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Tallymer-occratio summarizes the occurrence ratios for a specified range of k-mer sizes within a set of sequences. Requires an enhanced suffix array (ESA) generated using Suffixerator.

Quick Start

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Test Data

Info

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

Input File(s)

Specify the directory containing the ESA files.  For example if you use the above example_data directory then the entry will end up being "/iplant/home/shared/iplantcollaborative/example_data/Tallymer/".

Then specify the root name of the ESA.  Using example_data you would enter "maize_BAC100".

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:
    • Minimum kmer length to report: Enter a number indicating the minimum k-mer length (nucleotides) to be reported in the analysis
    • Maximum kmer length to report: Enter a number indicating the maximum k-mer length (nucleotides) to be reported in the analysis
    • Path to the directory containing the enhanced suffix array (ESA): Browse to the directory containing the ESA files
    • ESA root name:  Enter the root name of the ESA, excluding the dot-3-letter suffix.  For example "Maize_BAC100"  for the example ESA in the example_data directory

Output File(s)

Expect a text file automatically named "occratio_output.txt".

Tool Source for App

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Include Page
docs:_DE_archived_apps_blurb
docs:_DE_archived_apps_blurb