Hi Ann, I am assuming that, as in your previous question, you want the sequence of the DMit loci grouped by regions (introns, coding exons, 5' UTR and 3' UTR). If not, please let us know. If so, you only need to make two small changes to the directions we previously provided. I have pasted the full set of directions below with the new revisions to get sequences (the two steps needing to be changed are marked with ***):
-------------- The best way to do this is to A) create a custom track of introns, another one of 5' UTR exons, another one of coding exons, etc and B) then sequentially intersect these custom tracks with the all_sts_primer table while filtering out the non-DMit records. A) First, let's create a custom track of 5' UTR exons. Go to the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) and select the following: clade: mammal genome: Mouse assembly: July 2007 (NCBI31/mm9) group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene region: genome output format: custom track and click "get output". On the next page, change the name at the top to be something like "5UTRknownGene", choose the "5' UTR exons" button and click "get custom track in table browser". Repeat the steps above for introns, coding exons (CDS) and 3' UTR Exons. Note that if you choose Exons, this will include both UTR and coding exons both. If you select "group: custom tracks" in the Table Browser, you should now see all of the tracks you just made in the "track" drop-down menu. B) Now, go back to the table browser and select the following: clade: mammal genome: Mouse assembly: July 2007 (NCBI31/mm9) group: Mapping and Sequencing Tracks track: STS Markers table: all_sts_primer region: genome filter: click on "create". At the bottom of the page, enter the following into the Free-form query section: qName like "%D%MIT%". Click "submit". intersection: click on "create". Select: group: Custom Tracks track: 5UTRknownGene (or whatever you named your track in step A) table: there will be only one table so there is no need to select one choose: "All all_sts_primer records that have any overlap with 5UTRknownGene" Click "submit". Now you should be back on the main Table Browser page. Select: ***output format: BED - browser extensible data and click "get output". You will be taken to an intermediate page entitled, "Output all_sts_primer as BED." There are some options on this page, but you do not need to make any adjustments or selections. ***Click "get sequence" at the bottom of the page to see your results. You should now have the sequences of the DMit loci that are located in the 5' UTR. Repeat B for your previously created custom tracks of introns, coding exons (CDS) and 3' UTR Exons. Note, that any DMit loci not found to be within 5' UTR Exons, introns, coding exons (CDS) or 3' UTR Exons are, necessarily, intergenic. ------------- Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Ann Eileen Miller Baker wrote, On 04/08/11 12:55: > 8Ap11 > Dear readers, > I am trying to find all amplified sequences of mouse DMit microsatellite > loci. > I looked over the mouse sections of your website, but didn't find. > Thanks for help. > Ann > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
