Hi Peter,
Sorry, I was using the MITObim pipeline. I forgot to mention this in the
original email. I had one input strain of a single set of reads. I am trying to
get our mitochondrial reference assembly and build out into the intergenic
regions for phylogenetics.
Pryce
On Friday, May 6, 2016 11:42 AM, Peter Cock <dmarc-noreply@xxxxxxxxxxxxx>
wrote:
Hi Pryce,
I can give you some quick partial answers...
MIRA can do multiple-strain assemblies at once, which is
where some of this starts to make sense. Did you have
more than one input strain? Sharing your manifest might
answer that - but usually there is only one.
Padded and unpadded is the sequences with and without
gap characters in the consensus where some of the reads
have extra bases. You'll probably want the unpadded FASTA,
depending on what comes next in your analysis.
Peter
On Fri, May 6, 2016 at 5:36 PM, Pryce Michener
<dmarc-noreply@xxxxxxxxxxxxx> wrote:
Hello,
Sorry if this is somewhere on the internet, I searched for a while and
looked through the readme, but I couldn't find anything that talked about
the different output files in the results folder. What's the difference
between the AllStrains, the readpool, and the reference output fastas? And
what's the difference between the unpadded and padded results?
Thank you,
Pryce Michener
