Thanks heaps Bastien, that is a great start, we will try it asap! We have a student here now looking into the detection of homopolymer errors; we will keep the list updated on what his findings are, and if there is anything that can help improving the assembly. Regards Björn On Tue, 28 Jul 2009 23:27:31 +0200 Bastien Chevreux <bach@xxxxxxxxxxxx> wrote: > On Samstag 25 Juli 2009 Björn Nystedt wrote: > > one thing that would be very nice to tag would be potential frameshifts in > > 454 data due to homopolymer errors. This would be a tag at sites where > > about half of the 454 reads call (the same) base and the rest call a gap > > (the cutoffs here could be discussed). In principle, these sites could have > > turned up in the SNP tag 'SAOc', but I don't think it does? > > Hello Björn, > > the S?Oc tags are reserved for SNPs between strains. But I've added a new tag > "DGPc": Dubious Gap Position on Consensus which is set whenever the number of > gaps is 40-60% (I didn't have time tonight to make that configurable) of the > number of bases from the next frequent base. > > Try version 3rc1a (which I've just uploaded) and tell me whether this suits > your needs. > > > In a hybrid assembly, this would also be sites where the basecalls from > > non-454 reads would be preferred in the consensus, even when 454 data > > dominate in coverage, so it could be used to automatically improve the > > consensus quality during the assembly, if this is not allready taken into > > account somehow? > > It is taken into account in hybrid assemblies already. Those site are tagged > STMS or STMU depending on whether MIRA thinks it could correctly resolve the > problem or not (although STMS and STMU are also set for differences not > involving gaps). > > Regards, > Bastien > > > -- > You have received this mail because you are subscribed to the mira_talk > mailing list. For information on how to subscribe or unsubscribe, please > visit http://www.chevreux.org/mira_mailinglists.html -- ==================================== Björn Nystedt PhD Student Molecular Evolution EBC, Uppsala University Norbyv. 18C, 752 36 Uppsala Sweden phone: +46 (0)18-471 45 88 email: Bjorn.Nystedt@xxxxxxxxx ==================================== -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html