Hi Ann, This is the step in where you are having trouble:
adding " quotation marks around %D%MIT% so the it became "D%MIT%" These were the instructions for this step: 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". You entered: "D%MIT%" The instructions state to enter: qName like "%D%MIT%" A separate off list email will be sent with an image to show you what that field should look like. If you have further questions, please send your email to: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Ann Eileen Miller Baker" <[email protected]> To: "Mary Goldman" <[email protected]>, [email protected] Sent: Wednesday, April 6, 2011 7:44:39 PM Subject: Re: [Genome] pls see attachment (has "printscreen" so you can follow my inputs) (see error message) 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 > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
