Hello, The output represents the same alignments, just different data points. PSL is also arranged by column, although the latter columns contain multiple values (comma separated) for exon blocks, which can increase the investment in creating parsing tools. Keep in mind that any of these can be uploaded into the browser as Custom tracks and some can be converted using the Table browser. A BED format may be a good compromise for you.
Some links: http://genome.ucsc.edu/FAQ/FAQblat http://genome.ucsc.edu/FAQ/FAQformat This should help explain a bit about the data fields. Jennifer Jackson ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Mera Vigyan" <[email protected]> wrote: > From: "Mera Vigyan" <[email protected]> > To: [email protected] > Sent: Wednesday, September 2, 2009 9:30:05 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] reg. blast8 format > > greetings > > what is the difference between running BLAT in normal psl format > and blast8 format ? > > The blast8 output is in tab delimited format which is similar to that > of > Blast and > easily parseable. > > Are blast8 and psl outputs same ? > I prefer the blast8 format. I hope it is fine. > > Mera > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
