Hi Shuli, For joining distant alignments generated by a local alignment tool like BLAT or lastz, the program axtChain (with -psl option) might be useful to you. Assuming you have a copy of our source tree, it's in kent/src/hg/mouseStuff/axtChain/ .
Angie ----- "Shuli Kang" <[email protected]> wrote: > From: "Shuli Kang" <[email protected]> > To: "Galt Barber" <[email protected]> > Cc: [email protected] > Sent: Monday, November 22, 2010 2:22:16 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] maxIntron option doesn't work? > > Thanks again, Galt. > > For queries with extremely long introns, I'm trying to combine BLAT hits > corresponding to upstream/downstream exons of the large intron into > one. This is the simplest way I can imagine... > > Best, > Shuli > > On 11/22/2010 02:10 PM, Galt Barber wrote: > > Hi, again, Shuli! > > > > We looked into this and spent quite a bit of time on it. > > It turns out that setting maxIntron to a smaller value > > indeed works reliably as promised. > > > > But setting maxIntron larger by itself does not > > make all longer exons possible. > > > > The reason is that the affine gap penalty for the large intron > > kicks in and blat decides not to chain further, despite the > > fact that maxIntron has not been exceeded. > > > > The only way to allow a larger maxIntron to accomplish > > anything would be to allow the users to change the > > gap penalties. At the time, Jim Kent, the author of BLAT, > > was not inclined to do so. > > > > If you have special requirements it might be possible to hack > > the source code to modify the gap open and extension scoring. > > > > However, we are unable to provide any advice on the specifics > > of how to do so. > > > > -Galt > > > > On 11/22/10 11:53, Shuli Kang wrote: > >> Hi all, > >> > >> I'm deal with some sequencing data. I have found a extremely large > >> intron (~ 1.5 Mb) generated by exon skipping events. I have tried > to > >> align this isoform to human genome but failed, no matter what > number I > >> have set "maxIntron" as. It seems that this option doesn't work at > all?? > >> > >> Someone had a similar post two years ago, but no response... > >> > >> Best, > >> Shuli > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
