Is there any useful infomation about how to use the TASSEL GBS pipeline for Paired end data

[xuan zhang]

TASSEL Team,

    Hi, Thanks for your exellent work on TASSEL! 

    I have illumina 100 PE GBS data for 250 F2 population. I am wondering how I can use tassel to the paired end data.

    Now, the TASSEL maybe support pair-end data,but I can not find any infomation how to use it. Is the any manual or pipeline to deal with my data?

    By the way,Can TASSEL 4.3.12 use the 100bp data on GBA pipeline?

  

best wishes

Xuan Zhang

[gautie...@cirad.fr]

I have the same question, no documentation for paired end handling in Tassel. The only available documentation is for Tassel3, but the current version is Tassel5.
However, by looking at the Javadoc I found the FastqToPETagCount Plugin. But when I try to run it I always have the same error message (with Tassel4 and Tassel5):

Max Available Memory Reported by JVM: 491 MB, even on a 32GB RAM computer.
I set Xmx to 512m just to see but of course with real data I set this threshold much higher. It seems that the program just take the Xmx parameter, lower it a bit and send this message, whatever you do.

So the question is, is Tassel really supporting paired end? And if it is, can we have access to some documentation or at least tutorial?

Best regards,

Gautier

[gautie...@cirad.fr]

By the way, the questions I saw on this forum about paired end are unanswered. One since august, the other since april.

https://groups.google.com/forum/#!searchin/tassel/paired$20end/tassel/7rT3v4H_7EE/os6LkN7YlCAJ

[Edward S. Buckler]

Fei Lu has developed pipelines that use PE. I don't know that they are ready for prime time. 

The new GBSv2 pipeline can handle variable length reads very easily. It is in testing now. 

Cheers 

Ed

Sent from my iP

On Dec 10, 2014, at 7:52 AM, "gautie...@cirad.fr" <gautie...@cirad.fr> wrote:

By the way, the questions I saw on this forum about paired end are unanswered. One since august, the other since april.

https://groups.google.com/forum/#!searchin/tassel/paired$20end/tassel/7rT3v4H_7EE/os6LkN7YlCAJ

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[xuan zhang]

Hi，ed

   Thanks for your responce, But I wonder when we can use the PE Tassel Pipeline, since It claimed that it is added to GBS pipeline more than one year ago.

   Is there any document I can refer to?

   Thank you very much!

best wishes

Xuan Zhang 

在 2014年12月10日星期三UTC+8下午11时31分41秒，Edward Buckler写道：

[Marcel Brun]

Hi Edward,

               I see that there are some plugins in GBS (Tassel 5) for PE, but it seems that the Network plugin (for UNEAK) does not support them yet. Is that right? Is there already an strategy for using the Network algorithm on PE data?

[Parul Agarwal]

Hello,

 

Can I use PE data on commandline TASSEL3.0-UNEAK pipeline yet?

[Edward S. Buckler]

The UNEAK pipeline is no longer under development, as it is much better to generate a poor quality pseudo-reference genome (2x300bp reads and makes 100,000s of small contigs).  

Sorry-

Ed

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/52b59638-f888-451f-a5be-ac45bde96e1b%40googlegroups.com.

[xyl]

I have not move to Tassel 5 GBSv2 yet. But planning to do so soon.

Until then ...

Does it make sense to treat the both ends as single reads for analysis? In theory, it 'doubles' the coverage on sites.

Thanks!