GenosToABHPlugin

[Adisu Negeri]

I am trying to convert ACGT format of GBS data to ABH format to use in R. But GenosToABHPlugin is not working for me. From my GBS data I have created one dataset for male parent, one dataset for female parent and then one dataset for all the progenies (parents are included in the progenies dataset). Then I clicked on progenies dataset then on AHB genotypes in TASSEL under data then selected the female parent and male parent then clicked ok. TASSEL is not returning error or result. Am I doing something wrong? Please help.
Thank you
Adisu.

[Jeff Glaubitz]

The input genotypes (including the parents) should all be in a single input file.  See:

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/GenosToABH/GenosToABHPlugin

 

Best,

 

Jeff

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[Adisu]

Hi Jeff

Thank you for your response. 

If I include both parents in the single input file how TASSEL knows which is the parent from list of genotypes included in the input file? 

When I click on ABH genotype plugin it asks for two input files: Parent A & Parent B. 

Thanks

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[Lynn Carol Johnson]

HI Adisu – You are correct that TASSEL expects parentA, parentB and the genotype data to be in separate files. Load the genotype file into the GUI, then click on data->ABH Genotype.  You will be prompted for an output file, the parentA and the parentB files.   When you click “ok”, a .csv file will be written to the specified output directory with the name you supplied.    Note the GUI does NOT add an extension, so please include the “.csv” extension with the name you supply.

I just tested and was able to run this from the GUI, creating a csv file that EXCEL was able to open.

Thanks - Lynn

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[Lynn Carol Johnson]

One more note – If you are still having problems, please turn on logging.  On the TASSEL GUI, click the “Help” button at the upper right corner, select “Logging”, and check “Debug level”.

You can also try running the plugin from the command line.  Please follow this link to see how to collect and send us debug information:

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf?rev=ceb7d48304e5562ecb3dc4eb7788a44c8fc23256

Thanks - Lynn

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[Stefan Reuscher]

Sorry for being absent here, I was on holidays.

Adisu,

The parentA and parentB file contain just the names of the parental samples, not the actual genotype data. This way you can put all data in one file and TASSEL knows which ones are your parents.

Cheers,

Stefan

[Lynn Carol Johnson]

From: Stefan Reuscher <reusche...@gmail.com>
Reply-To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Date: Sunday, June 14, 2015 at 7:22 PM
To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Subject: Re: [TASSEL-Group] GenosToABHPlugin

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/9f1115bf-ebf8-4a1b-b283-df74e069191b%40googlegroups.com.

[Adisu]

Hi Stefan

You answered the critical question. I have tried this morning & TASSEL converted my ACGT format data to ABH. Thank you for your great input. I like to thank you Jeff & all others helping people using TASSEL.

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