The psl output shows the native blat output with exons (aligning regions) chained together with introns (gaps) between them.
When you choose blast output, each exon is reported by itself with no chaining. As far as why the scores look different, that's just due to the way the psl and blast formats are defined differently. -Galt 9/29/2011 7:03 AM, Fathepure, Shakuntala: > > I used blat on my custom reference and query sequence in command line. I have two output files from blat. One is psl and other is blast format. When I compared the results it looks different, there are no matches above 124 and below 34 in psl. Blast format output result has higher of 272 and low of 12. Why is it so different? I have not changed any parameter, everything is in default. I appreciate help from you. > > Thank you, > Shakuntala Fathepure > Dept. of Botany > Oklahoma State University > Stillwater, OK 74078 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
