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.
Thanks for the great feedback, sorry there wasn't a solution (yet!),
On 7/22/11 12:56 PM, David Matthews wrote:
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
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