Hi Shakuntala, Please see this BLAT help section:
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign You will likely want to run BLAT from the command line since it sounds like you have your own reference sequence you want to compare to. Here is more information on the command line version of BLAT: http://genome.ucsc.edu/goldenPath/help/blatSpec.html I hope this clarifies things for you. If you have further questions, please contact the mailing list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Fathepure, Shakuntala <[email protected]> Date: Wed, Jul 20, 2011 at 7:25 PM Subject: [Genome] BLAT To: "[email protected]" <[email protected]> Cc: "[email protected]" <[email protected]> I am trying to use BLAT to blast short reads(FASTQ) from the NCBI, SRA with my custom reference sequence(fasta format) to check the hits and then design primers. I am bit confused how to use the program efficiently. I am planning to read the help to find solutiosn. I would really appreciate, if you can help me with the above situation. Thank you, Shakuntala Fathepure Postdoc 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
