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
