Hi John,

That would be totally fantastic - many thanks!


Best Wishes,
David.

__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk






On 30 Jul 2011, at 16:35, John Nash wrote:

> I have some code which can do most of the requested things. Let me figure out 
> how to galaxy around it, and I'll submit it.
> 
> John
> 
> Sent from my mobile device
> 
> On 2011-07-30, at 12:47 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
> 
>> Hello David,
>> 
>> Generating a consensus fasta sequence from a BAM or Pile-up file is not yet 
>> possible in Galaxy. To date, the Tool Shed also does not have a 
>> wrapped/novel tool for this function either.
>> 
>> If you or another user were to create such a wrapped tool, it would be most 
>> welcome. As would a tool that would replace the corresponding region of the 
>> reference genome with the variant fasta sequence to create a novel reference 
>> for alignments.
>> 
>> Both great ideas that have been discussed a few times on the list and here 
>> among our team. If you wanted to open a bitbucket ticket, that would be one 
>> way to share exactly what you had in mind and give you a ticket to watch for 
>> if/when tools like this are added. Or, I can open one (or possibly two, one 
>> for each function) for you, just let me know.
>> 
>> https://bitbucket.org/galaxy/galaxy-central/issues?status=new&status=open
>> 
>> Thanks for the great feedback, sorry there wasn't a solution (yet!),
>> 
>> Best,
>> 
>> Jen
>> Galaxy team
>> 
>> 
>> On 7/22/11 12:56 PM, David Matthews wrote:
>>> Hi
>>> 
>>> On a separate issue, I have been having trouble generating a corrected 
>>> fasta file based on a pileup. I have a dataset that is a resequenced genome 
>>> and I want to correct the fasta file based on the consensus and then re run 
>>> the alignments to see how it affects things. However, I cannot for the life 
>>> of me figure out how to do it in Galaxy. Any help appreciated!
>>> 
>>> David
>>> 
>>> 
>>> 
>>> ___________________________________________________________
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>>> 
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>> 
>> -- 
>> Jennifer Jackson
>> http://usegalaxy.org
>> http://galaxyproject.org/Support
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
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>> at usegalaxy.org.  Please keep all replies on the list by
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>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>> 
>> http://lists.bx.psu.edu/
> 
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
>  http://lists.bx.psu.edu/

___________________________________________________________
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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