[mira_talk] Re: Question on mapping PacBio reads to reference
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 03 Oct 2013 22:10:53 +0200
On 10/03/2013 09:33 PM, Foecking, Mark F. wrote:
Hello. We have a set of scaffolds that were generated from PacBio
reads for a small genome, and we are trying to map these reads using
the scaffolds as a reference, so we can view the resulting .ace file
as a pileup in EagleView and look at frameshifts and SNPs and perhaps
determine if they are real or not (without PCR/sequencing).
EagleView? ACE file? Maybe you want to use different tools ... just
saying :-)
When we do this, some of the reads map to the reference (perhaps
10-15% of them) but when we open the file in EagleView, we find the
reference sequence has changed -- is MIRA making a new consensus and
showing that alignment?
Ummm, no, MIRA does not touch the reference sequence. Never. Maybe
EagleView is recomputing a consensus on the fly?
Is there a way of having the reads aligned to the original scaffolds?
They're always aligned to the original data :-)
Have you tried different viewers? gap4? gap5? Tablet?
B.
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