Hello Dafil, The genome sequences on the Downloads server contain soft-masked files. All bases are present (not hard masked as "NNN"). Many alignment programs has settings that specify to ignore soft masking (including BLAT). Another option is to convert all of the bases to upper case with a simple script.
For hg18, the sequences are located on the Downloads server at: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/ The README files explain the available file formats and how to use anonymous ftp or rsync. I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support On 7/20/10 8:27 PM, [email protected] wrote: > Hi, > I am just wondering where can I get hg18 UNMASKED genome fasta or .fa files? i > have mapped my reads against hg18 masked .fa but i need to do it in unmasked > genome. > please help. > > regards, > -dafil > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
