To whom it may concern: I am doing some analysis in honey bee genome and I come across some problem that need your help. What I do is to run blat in my local server and get the pls format output file which record the coordinates of the alignment block . But the problem is the database file I downloaded is the scaffold sequence for honey bee genome in UCSC table browser which under the scaffold track. After searching against this database, I compared the output to the result I searched in web-base blat, it turned out that the output for a same refseq ID has the same hit but different coordinates, I think the difference is due to different coordinates system(one based on linkage group and the other based on a certain scaffold.) In this case I can't extract the right sequence based on the scaffold coordinates. So, I was wondering if there is a resource like the sequence for a whole linkage group I can use as the database? Thank you !
Jia _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
