[mira_talk] Questions regarding the paired-end distance calculation done by MIRA
- From: "Bayles, Darrell" <Darrell.Bayles@xxxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 28 Jan 2011 15:41:11 -0700
I've been working on an assembly of 454 data that contains a mix of
shotgun and paired-end reads. The paired end reads have been
empirically mapped and have a calculated distance of 3000 bp with a
standard deviation of 800 bp. All that information gets put into the
traceinfo.xml file in the usual fashion, but the distance range that
MIRA indicates its actually using is quite a bit larger than I expect.
Bastien previously posted
(//www.freelists.org/post/mira_talk/TF-and-TT-in-MAF-format,3) that
he has built in a '"lenience" factor' that allows for 20 or 30%
deviation. Was the actual value pinned down?
For the experiment that I mentioned, the *out.caf file indicates MIRA
has given the paired reads the allowable minimum distance of 600 bp and
maximum of 5400 bp. That still gives a mean of 3000 but with a
deviation of 2400 bp. I also looked at a previous experiment where the
pairs were defined as having a mean of 7200 bp and a standard deviation
of 1800 bp. MIRA output indicates that it is using a range of 1800 bp
to 12600 bp. That would indicate a mean of 7200 bp and a deviation of
5400 bp. In both cases it appears that MIRA is not using a percentage
factor, but is actually using three standard deviations. Does that
sound correct Bastien?
I'd like to be able to reign in that value, and can probably do it by
indicating an artificially smaller standard deviation in the input
traceinfo.xml file, but does anyone know if that "lenience factor" can
be modified directly?
Regards,
Darrell
==========================================
Darrell O. Bayles, M.S., Ph.D.
USDA, ARS, National Animal Disease Center
Infectious Bacterial Diseases Research Unit
1920 Dayton Ave, Bldg 24
P.O. Box 70
Ames, IA 50010
Tel: (515) 337-7165
Fax: (515) 337-7002
==========================================
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