[mira_talk] Re: force MIRA to produce only singletons and no debris
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 21 Feb 2011 15:23:42 +0000
On 21/02/11 10:02, Yvan Wenger wrote:
[...]
I am satisfied with the assembly itself, but performing a blast tells
me that 1437 sanger reads I inputed do not have any counterpart in the
cleaned_out.unpadded.fasta file... how can that be? On what basis are
these sequences discarded? I will end up fetching all those sanger
input that do not have a hit in the final fasta file produced, but I
am still curious.
Hi, Yvan.
How did you create your Sanger contigs?
I would try a mapping assembly to see where the 454 reads map onto the
Sanger contigs, used as a 'backbone' instead of Sanger pseudo-reads.
However, I think that it's possible the other assembler you used to
create the Sanger contigs has collapsed repeats that MIRA resolved.
Unless, of course, your other assembler was MIRA ;-)
Bye,
Tony.
--
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis@xxxxxxxxxx, http://bioinformatics.rri.sari.ac.uk
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