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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