GBS tag in TASSEL 5 v2 pipeline

[batten...@gmail.com]

Hi,

I am trying to extract GBS tags from a v2 pipeline run. 

I have tried the GetTagSequenceFromDBPlugin, but it returned all tags with no identifying information.  I would also like the alleleid, snpid, position and chromosome number so that I can merge these with the SNPs we are using in some analysis. 

I also tried using SQLite to access the sequences directly from the GBS.db, but it seems like they are encrypted and converted into blob format.  I've gotten them out of blob format, but still not human readable.

Would it be possible to access the source code to GetTagSequenceFromDBPlugin to see how to convert this data into DNA sequence?  Is there another way to access tags with other identifying information?

Thanks for your help,
Sarah

[Lynn Carol Johnson]

Hi Sarah -

You can download all the TASSEL source code from our web site:

http://www.maizegenetics.net

Click on the “TASSEL” link and you’ll find instructions.

Thanks - Lynn

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[batten...@gmail.com]

Hi Lynn,

Thanks, I've been searching for this for a while.  Specifically, I'm looking for the code for this plugin

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline/GetTagSequenceFromDBPlugin

Could you link me to that one?
Thanks,
Sarah

[Terry Casstevens]

https://bitbucket.org/tasseladmin/tassel-5-source/src

> https://groups.google.com/d/msgid/tassel/ebaeb37c-cc1b-410c-9718-cde8710e8b0a%40googlegroups.com.

[Sarah Battenfield]

Hi Terry,

I may not be asking for this correctly, but what I'm looking for is the way to decode the sequences stored in GBSv2 database as human readable.  I've done SQLite queries and gotten all the other identifying information that I need to merge positions to the GBS tag, except the tag itself.  If I use GetTagSequenceFromDBPlugin, that is the kind of output I want, but also need tagid so I can join it with the position.  Can GetTagSequenceFromDBPlugin be updated to also output tagid?  Is there a way to output 'sequence' in 'tag' table directly in SQLite?

Thanks,

Sarah

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[Terry Casstevens]

Hi Sarah,

I don't know the answer to that. The link I sent is the source code
which includes that plugin. I thought you were asking for the source
code.

Terry

> https://groups.google.com/d/msgid/tassel/CAKvMvc5u4gRSeW9ZfgG-DV5yzVBUzDpBi63M_a94ukXKm-qokw%40mail.gmail.com.

[Sarah Battenfield]

Hi Terry,

Yes, I was looking for source code to see if I could figure out how GetTagSequenceFromDBPlugin was making the sequence human readable. 

This is the link to the specific source code, documented for anyone else reading this forum: https://bitbucket.org/tasseladmin/tassel-5-source/src/b1f8c4318cbe8fb22c97d00efef071d2a90d8069/src/net/maizegenetics/analysis/gbs/v2/GetTagSequenceFromDBPlugin.java?at=master

My java is poor, but it looks like I would need a patch somewhere in lines 80-110? to also request and print a string of the tagid as well.  Is this possible?

Thanks,

Sarah

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[Sarah Battenfield]

Terry,

Is there a hash table for sequences?

Thanks,

Sarah

[Lynn Carol Johnson]

HI Sarah -

No, there is no hash table for sequences.  

At present, we don’t have time to change the code as you request, though it is open source and you are welcome to make changes yourself.  If you look at the code under maize genetics/dna/tag you will see how the Tag object is defined.  You can look at current GBSV2 database queries in file maize genetics/dna/TagDataSQLite.java to get an idea of how to match tagid and other data in the db.  

Lynn

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