Hello, Perhaps intron regions are being confused with actual base gaps in exon regions? If you are comparing a sequence that has splicing to a genome, it is an important distinction.
If you want to send a sample alignment output that is not what you were expecting, please paste it into an email, send just to me, and note where you believe the problem is. Include the query also, please, in fasta format. And note which genome, so that I can duplicate the run. The smaller the sample, the better. Or, upload the example as a Custom track, add to a Session, and send me the url from the Session tool. After that, we can provide help interpretting the data or offer recomindations for tuning BLAT. Meanwhile, BLAT help is here: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Ji-Ping Wang" <[email protected]> wrote: > From: "Ji-Ping Wang" <[email protected]> > To: [email protected] > Sent: Thursday, February 4, 2010 6:48:39 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] How to use blat to obtain alignment without gaps > > Hi, > > Can anyone help on how to generate local alignment without gaps > using > blat? I try to use commands as follows: > > blat seq1.fa seq2.fa -minIdentity=100 -maxGap=0 out.psl > > always generate alignment with gaps. > > Thanks. > > Jiping wang > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
