[mira_talk] Problem template names and FR naming?
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 30 Nov 2011 17:18:16 +0000
Hi all,
I have some Sanger reads with names like this:
WT-13_M13.FW
WT-13_M13.RV
That is the forward and reverse reads for a primer pair named
WT-13-M13, using suffixes of .FW for forward and .RV for reverse,
so I invoked MIRA with switch -LR:rns=fr for the *.f* and *.r* naming.
Thankfully the case doesn't seem to matter.
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
DI F
SF WT-13_M13.FW.scf
...
and:
RD WT-13_M13.RV
...
TN WT-13_M13_V
DI R
SF WT-13_M13.RV.scf
QR 945
...
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?
It isn't critical for me as I can (and have) renamed all the reads
to use just .F and .R instead, and that seems to solve this.
Thanks,
Peter
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