[mira_talk] Re: Mappging to Reference
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 10 Jun 2010 18:40:39 +0200
On Donnerstag 10 Juni 2010 Saulo Alves wrote:
> I'm facing a problem where I'm trying to map all the "events" on the query
> sequence (the new genome) to the reference genome.
Hello Saulo,
I'm not sure I can follow you. What are "events"?
> The problem is, MIRA inserts several * on the reference prior to assembly
> and shift frames (as reported in the AT field in the MAF file).
Well, looking at a case like this:
ref ....acgta*cgt....
s1 ....acgtaGcgt....
s2 ....acgtaGcgt....
s3 ....acgtaGcgt....
s4 ....acgtaGcgt....
s5 ....acgtaGcgt....
then why should MIRA not insert a gap? This is what makes most sense and
reflects accurately the change of the new genome against the reference.
> After all those modification I'm not able to map BACK base-by-base each
> problem.
You can parse the positions with gaps in the reference sequence by looking at
"AO" lines in the reference reads. It's pretty easy actually: fill an array
with "-1", then apply all "AO" line from the reference read. Positions having
"-1" at the end of this procedure are gaps. From there, creating a mapping to
your original sequence is a breeze.
> I'm planning on creating a "multiple alignment" of the two sequences for
> high density annotation.
This actually I do not understand: what do you want to do?
Regards,
Bastien
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