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
