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=newstatus=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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