Hi Galt, thank you for the quick answer, I prefer programs to scripts. Did I understand correctly that the sketched scenario of 10% of a trancript aligning with the same identity as 100% of a transcript and both alignments are kept occurs at UCSC? Is it frequent?
Thank you, micha. En/na Galt Barber ha escrit: > > Percent Identity only applies regions aligned. > Gaps are not considered aligned regions of course. > > You are interested in the level of coverage. > You can use utilities like pslReps and pslCDnaFilter > to post-filter your BLAT psl results. You can also > just write your own script to filter it however you like. > > You might also try the BLAT options -maxGap=0 and -fastMap. > > -Galt > > > On Mon, 10 Nov 2008, Micha Sammeth wrote: > >> Hello helpdesk, >> >> I have again a curiosity concerning blat alignments. I consider the case >> BM451627. It was for some reasons not in the dataset of hg17, so I >> downloaded the sequence and ran a blat -stepSize=5 -minScore=0 >> -minIdentity=0, which should correspond to the settings used at UCSC. >> Checking idendity, I find the highest score of about 20% sequence >> identity -- match/query length -- it also does not change much when >> additionally taking into account repmatch. >> >> However, I found BM451627 in the UCSC hg16 database, where it reports a >> ~98% identity match. Looking closer at the alignment, in hg16 there is a >> ~150nt stretch from the 1244nt which aligns with 98% identity --- and >> probably a couple of bases that changed from hg16->hg17 are responsible >> that in this 150nt region sequence identity drops below the threshold of >> 96%. >> >> My question now is: >> >> Does this hold for all identities, say a transcript aligns with 1000 nt >> and 98% identity in one place and in another place with 100nt at 98% >> will be put in both places, regardless of the coverage of the transcript >> by the alignment? In other words, the identity criterion of 96% or 0.5% >> of the best alignment is applied to match/(Qend-Qstart)? And if so, what >> was the motivation to not take the "global identity" of the query, did >> you have bad experiences with transcripts that did not want to align >> that way? >> >> Thank you! >> >> micha. >> >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome >> > -- O o O o O o Dr. Michael Sammeth | O o | | O o | | O o | http://www.sammeth.net | | O | | | | O | GRIB| O | Phone: +34-933-160-166 | o O | | o O | | o O | Fax: +34 933-969-983 o O o O o O Dr. Aiguader 88, 08003 Barcelona _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
