Hi Shakuntala, One of our engineers also had this to say:
You might want to consider if blat is the appropriate mapping tool for short reads. It may work if their reads are long enough, but I believe the short read community has better aligners for this type of work. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group On Thu, Jul 21, 2011 at 3:57 PM, Vanessa Kirkup Swing <[email protected]> wrote: > 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
