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Select Markers to Keep v1

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With this tool and based on the quality analysis done in a previous step with the Filter Genotypes app, the number of markers to keep for further analysis will be selected.

Quick Start

  • To use Select Markers to Keep, your data need to be in csv format. There should at the left part of the csv document two columns one the name of the samples and the very next one any other description of the sample e.g. the population where samples belong. The next columns can be the Genotypes. Missing Genotypes are denoted with NA. In the number of markers having number of samples field,based on the evaluation done in a previous quality analysis, user decides the minimum number of samples each marker should have by default we have 40

Test Data

Info

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

Input File(s)

Use TestingData.csv from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the default parameters with the above input file(s) to get the output provided in the next section below.

Output File(s)

Expect a text file with the filtered number of markers.  For the test case, the output file you will find in the example_data directory is named filtered data final.txt 

 

Include Page
docs:_DE_archived_apps_blurb
docs:_DE_archived_apps_blurb