Hello again, To add a bit more information if you are examining data directly from the Affy Exon track, sub-track Probe, the primary table affyAllExonProbes:
The data format is BED6 (ignore the leading column called "bin" as it is used for database indexing only). BED format is defined here: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 Please see the track description for how to interpret the column name, which can be used to sort out the various data types included. The rows represent individual exons. To export the coordinate data, within the table browser navigate to the table, set the region to be chr6:80681498080,898, and select output as primary table. To export sequence data, select output as "fasta". Pasting in/uploading multiple regions is also an option. You could also add in a filter on the name column or you can filter the data after it is downloaded. If your intention is to retrieve the entire table, use the Downloads server and ftp/rsync the file affyAllExonProbes.txt.gz from here: http://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/ For multiple sequence regions, you can also download the entire genome sequence (there are a few different formats), use a utility from the kent source tree and the coordinates in the BED file output/download, and extract regions in batch. The format of the genomic sequence will determine which utility to use. For example, if using a fasta format try faSomeRecords. http://genome.ucsc.edu/FAQ/FAQdownloads.html#download32 http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download Genome sequence data: http://hgdownload.cse.ucsc.edu/goldenPath/rn4/bigZips/ Compiled binaries: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ Utilities can be also obtained from the kent source tree and compiled locally on your system: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download27 Downloading through a browser from the hgdownload server is not recommended. The links to hgdownload are to help you locate the path to the data when using ftp/rsync. Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ > On 2/12/10 9:42 AM, Athippozhy, Antony T wrote: >> To whom it may concern, >> I contacted Affymetrix regarding locating the start and stop sites of exons >> on their Rat Exon chip. They redirected me to the UCSC genome browser and >> told me to check your database for exon locations. I checked the rat build >> Nov. 2004, Chr. 6 8068149-8080898 and called up your entry for the rat ABCG8 >> gene. Exons are identified as boxes. How do I call up a table or some >> other display that clearly displays the exon start and stop sites. I called >> up a table, but there appear to be more entries in the table than there are >> exons in the gene. HOw are these entries organized? >> >> Sincerely, >> Antony Athippozhy >> >> _______________________________________________ >> 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
