Hello Matthew, Can you send some sample input and output from using your local Blat server? Strand *should* be indicated in column 9 of the PSL output from blat (described here: http://genome.ucsc.edu/FAQ/FAQformat#format2).
-- Brooke Rhead UCSC Genome Bioinformatics Group On 01/01/09 14:45, Matthew Schu wrote: > I set up a local Blat server using the instructions given in the FAQ section > of your website. I expected the results from my query to be in psl format, > but the data that was returned lacked a column indicating the strand (either > "+" or "-") for the match. I used a command similar to the one given on the > website: > blat -stepSize=5 -minScore=0 -minIdentity=0 database.2bit query.fa > output.psl > > Can anyone tell me why I didn't get the strand entry for any of my results, > or perhaps suggest another way to retrieve this information from the > database? > > Thank you, > > Matt Schu > Bioinformatics Grad Student > Boston University > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
