Hi Ann, I'm very sorry, but while your message is different, your screen shots look identical to those that you sent before!
I think it might be a good idea to start from scratch. It's possible to clear all settings and erase all custom tracks from the Genome Browser by clicking on the "click here" in the line at near the bottom of the table browser "To reset all user cart settings (including custom tracks), click here." I suggest doing that first. Below are the same instructions as before, with the previous corrections included. When I went through these instructions for 5' UTR regions I got 26 lines of output. -------------- 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 BED" at the bottom of the page to see your results. The fourth column should be the names 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. ------------- I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 4/4/11 8:40 PM, Ann Eileen Miller Baker wrote: > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
