When you choose blast output, BLAT breaks the alignment which it made so that one blast record is created for each exon.
If you want to keep them chained together, use psl format. Because blat applies minIdentity to the entire alignment as a whole, you may find with blast output that some of the individual exons are below 98% identity. -Galt 5/4/2011 4:20 PM, Quanwei Zhang: > Dear Dear Sir/Ms: > > We have created a standalone BLAT on our computer. We are confused by the > following > results when we use it. > > 1) When we set the parameter -minIdentity=98, it does not work. Blat show us > all the > aligns even its identity is below 98. So would you please tell me why? > We do it like this: > ./blat hg19.fa query.fa aligns.txt -fine -q=rna -minIdentity=98 -out=blast8 > > 2) The web Blat can work well when the reads extend introns(i.e. the read is > from > different exons). However, when we used the standalone BLAT, it can not align > to two > exons or more. Would you please tell me what we should do to make the > standalone > BLAT work well as the web blat? Our reads are cDNA reads. > > Are there some kind software by which can make us use the web Blat (i.e. > program-driven use of blat)? > > Thanks > > Best > Quanwei > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
