[mira_talk] Re: Unpaired read in mapping assembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 06 May 2012 20:09:57 +0200
On 05/05/2012 02:44 AM, Arnav Moudgil wrote:
I'm trying to detect indels in a mapping assembly of paired-end Solexa
reads. In genes with very small indels (i.e. 1 bp), MIRA calls the
indels correctly. However, another gene I'm looking at has a 22 bp
deletion. When I run the mapping assembly, the indel isn't called;
instead, where the indel should be is a single, unpaired read (i.e.
its mate is not in the assembly). Is there a way to exclude all
unpaired reads from the assembly?
Hello Arnav,
no, there is not. I did not have the need for something like this until now.
Would this help call such an indel?
No, it would not. On the contrary, I suppose it would weaken the
assembly by throwing out the mates which could be matching perfectly fine.
The manual states that indels should be 10-12% of the read length for
reliable calling, but the reads going into this assembly are about 120
bp long. A non-ideal situation, so any help would be appreciated.
There's one question I have: how are you trying to detect those larger
InDel? Algorithmically will be difficult, but if you do not mind doing
this semi-automatically, then you could do what I do for all data sets
going through my hands: look out for problematic areas using a viewer
(i.e. gap4 / gap5) and searching for tags set by MIRA. See
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_sxa_postprocessing_mapping_assemblies
for more info.
HTH,
B.
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