[mira_talk] Re: Problem template names and FR naming?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 30 Nov 2011 20:31:54 +0100
On Nov 30, 2011, at 18:18 , Peter Cock wrote:
> I have some Sanger reads with names like this:
> WT-13_M13.FW
> WT-13_M13.RV
> [...]
> I assembled this with MIRA 3.4.0, but noticed a problem in the MAF output
> (well, actually the problem with after converting with maf2sam.py and not
> seeing the pairs I expected), where I see:
> RD WT-13_M13.FW
> TN WT-13_M13_W
> and:
> RD WT-13_M13.RV
> TN WT-13_M13_V
> So clearly MIRA is understanding the directions (DI lines look fine)
> but something is going wrong (or at least counter to my expectation)
> in selecting the template names (TN), with the arbitrary text after
> the F or R being included. Have I found a minor bug?
I had to shortly think what it is what you actually found, but - nope - it's
not a bug, it's one of the undocumented features and works as designed.
Background: sequencing centers had - in ye olde Sanger times - the possibility
to redo a (paired-end) sequencing of a given clone, sometimes with a changed
chemistry to tackle difficult areas. The read naming (at least from the Sanger
Center and TIGR) had different building blocks and was in general a bit like
this:
ReadTemplate---PairedEndQualifier---FurtherCodingDenotingSequencingAttemptAndChemistry
To keep things simple and have only two reads per template, MIRA builds out of
this a new template name like this:
ReadTemplate---FurtherCodingDenotingSequencingAttemptAndChemistry
A coupe of years ago I told MIRA to use the method for the (initially 454) F/R
naming scheme because the paired-end data there sometimes contains other
fragments and I got them out of the equation using the same trickery. That's
what you are seeing.
I do agree that it might be a bit unexpected with the F/R naming scheme, one of
the oddities I'm not sure I want to find a way around because of decreasing
Sanger importance and the fix being so easy: stick to the naming scheme :-)
B.
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