The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Tassel3 Conversion

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This application harnesses the conversion capabilities of the Tassel 3 pipeline in order to facilitate conversion of common GWAS file formats.

Quick Start

  • Select the expandable menu that matches your input file format. 
  • Upload all required input files within that menu. 
  • Select the Output expandable menu (it will be the last expandable menu option).
  • Select the file-format that matches the format you would like to export to from the drop-down list. 
  • Launch analysis. Once the conversion is completed the converted file will be found within the relevant analysis sub-folder as converted.(your format extension).
  • Resources: http://www.maizegenetics.net/tassel/docs/TasselPipelineCLI.pdf

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Tassel3 Conversion.

Available Input Formats

Format

Extension(s)

HapMap

.hmp.txt

PLINK

.map, .ped

Flapjack

.map, .geno

FASTA

.fas

BLOB

.zip, .gz

Genetic Map

.map, .txt

Available Export Formats

Format

Extension(s)

HapMap

.hmp.txt

HapMap Diploid

.hmp.txt

PLINK

.map, .ped

BLOB

.zip, .gz

Flapjack

.map, .geno

Phylip (Sequential)

.phy or .ph

Phylip (Interleaved)

.phy or .ph

Tab Delimited Text

.txt

Tool Source for App

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