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
