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 <jen@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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___________________________________________________________
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/