Hi Jeffrey, The .2bit format for the Chimp genome assembly is soft masked. To use blat with this .2bit file please see this previous mailing list question:
https://lists.soe.ucsc.edu/pipermail/genome/2007-March/013054.html For information about files for panTro2 you can look here: http://hgdownload.cse.ucsc.edu/goldenPath/panTro2/bigZips/ The .2bit file is missing in this documentation. We will look into having that added to our documentation. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Jeffrey Pratap Vedanayagam" <[email protected]> To: [email protected] Sent: Friday, July 16, 2010 11:02:03 AM GMT -08:00 US/Canada Pacific Subject: [Genome] query regarding chimp assembly Hello, I was just wondering if the the Chimp genome assembly in .2bit format is RepeatMasked or not? Reason: When I do a BLAT search on the chimp genomic sequence in .2bit format, I do not see any genomic hits for my query, but if I do the same on the RepeatMasked genomic data (sequences of genomic repeats in chimps), I do find a match. Thanks, Jeffrey _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
