6Ap11 1943 (please see new PRINTSCREEN attachment to help you pinpoint my error) Dear SOE group and Mary Goldman, 1. I want to thank all of you for your help and patience. 2. Mary, the only difference btwn the first PRINTSCREEN and the second PRINTSCREEN was adding " quotation marks around %D%MIT% so the it became "D%MIT%" 3. I retry multiple times (guestimating at least 40X total) before emailing; today I followed your detailed valuable directions 4X before sending this as a PRINTSCREEN: though I did fresh PRINTSCREEN because I was following the directions you sent today, there is no differrence btween this third PRINTSCREEN and the second PRINTSCREEN - this is why I request someone @ SOE looking hard at what I am doing because I am following your directions to the best of my ability and still fail. 5. I keep failing, though Mary gets the correct output. Note that I am only running 5UTR until I show myself that I can get output. Further, since there are ca. 7500 DMIT amplified sequences, I feel there should be 7500 5UTR, whereas Mary mentions getting only26 5UTR if I understood her. 6. If someone has the time, I would be grateful if the person pinpointed where I am going wrong. Note each time I start from scratch using CLICK HERE (reset). I am extremely sorry to take all your time, but I keep failing and don't know where else to turn: doing these analyses are still complex for me. I also had my husband try follow these directions, but he also fails to get an output: we are both smart, used to following complex directions. Respectfully, Ann
On Wed, Apr 6, 2011 at 6:15 PM, Mary Goldman <[email protected]> wrote: > 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 > >
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