Update: One of our scientific engineers reminded me that we have tools in the source tree to help with masking: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities
* maskOutFa (takes .bed file w/coords) * twoBitMask Download the source here: http://hgdownload.cse.ucsc.edu/downloads.html scroll down to "Source Downloads" -> "UCSC Genome Browser source download" These utilities are not in the set of pre-compiled utilities on the downloads server, so you will need to follow the instructions in the READMEs and linked help documents. Perhaps this will be help you avoid having to create your own tool(s) for the masking step, if you decide to try this method. Best wishes, Jen On 6/1/10 9:57 AM, Jennifer Jackson wrote: > Hello Vera, > > Yes, this is possible, but you will need to obtain the reference genome > sequence, coordinates that you want to mask, do the masking, then run > BLAT on your own server against the newly created file. > > (using hg19 as an example in links, if using hg18, swap in that database > for the links). > > FTP sequence: > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ > > Obtain CDS coordinates: > Use Table browser or Downloads server, a Gene Prediction track (UCSC > Genes, RefSeq Genes, CCDS, etc.), and output or ftp the CDS coordinates. > > Table browser (good even if using FTP to learn table > names/fields. See track descriptions to review methods > and select proper dataset for your purposes). > http://genome.ucsc.edu/cgi-bin/hgTables > http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html > > Ftp complete files (representing mySQL tables): > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ > > > BLAT: > http://genome.ucsc.edu/FAQ/FAQblat.html > > Hopefully this will help you to get started, please let us know if you > need more help, > > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 6/1/10 8:58 AM, Vera Pendino wrote: >> Hi, >> I would like to run blat with a short sequence on the regions that are >> annotated as intronic, intergenic and UTRs in the human genome(hg19). >> In other words, I'd like to know if it is possible to mask the coding >> regions of the genome. >> Could you help me? >> thank you >> >> Vera >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
