Hi Ann, I am glad you are finding the website to be a useful resource. Thank you for all of your suggestions about it and about our user support methods. I have passed them on to our management team for review and consideration.
I am also glad you found the Open Helix video tutorials helpful. In case you want to refer to them again in the future, the links to these videos and other helpful guides can be found by clicking the "Training" link (in blue left-hand menu) on our home page (genome.ucsc.edu). The Training link takes you here: http://genome.ucsc.edu/training.html. Your suggestion to make these videos easier to find has been passed on to our management (along with your other suggestions as I described above). Regarding the "submit" vs "get output" button. I'm sorry for the confusion this mix-up caused you! In section "A)" of her instructions, Mary did accidentally direct you to click "submit" instead of "get output." I'm glad you were able to deduce that "get output" was the correct button. Now, I would like to address your error message, which I was able to reproduce. In section "B)" of Mary's instructions, you set up a filter. I have pasted Mary's directions from section "B)" for creating the filter here: filter: click on "create". At the bottom of the page, enter the following into the Free-form query section: qName like "%D1MIT%". Click "submit". One change I need to make to the part of the instructions pasted above is that the numeral 1 in the query needs to be changed to a % character; so you need to type the following into the Free-form query: qName like "%D%MIT%" Please be sure to type the entire string into the Free-form query: qName like "%D%MIT%" I was able to reproduce your error when I just typed in the last part:%DMit% One thing to be cautious of, once you are back on the main table browser page, if you click the "edit" button next to filter, double check your Free-form query. When I did this, I noticed that this, qName like "%D%MIT%", was truncated to, qName like. This is a small bug that I have reported to our development team. If you do click edit, please be sure to check your Free-form query and, if it was truncated, please re-enter the complete string: qName like "%D%MIT%" Another thing I would like to mention has to do with Mary's original instructions. Her instructions are extremely thorough, however, while troubleshooting your error message, I did notice a small step was missing. In section "B)", between these two steps: > and click "get output". > > 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. Any DMit loci > not found to be within 5' UTR Exons, introns, coding exons (CDS) or 3' > UTR Exons, are necessarily intergenic. After you click "get output," you'll 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. Simply click "get BED" at the bottom of the page to see your results. Then, continue following Mary's instructions. I hope this is helpful! Please contact the mail list ([email protected]) again if you have a specific question. Katrina Learned UCSC Genome Bioinformatics Group Ann Eileen Miller Baker wrote, On 03/31/11 22:41: > 31Mr11 2239 > I tried to find table browser introduction but got stuck in advance helix > (advance table browser; i bounced around the > website w/o luck; now try google...putting in "table browser introduction"- > just looked; keep going in circles w/o finding > introduction (assume it is also dvd like the advanced table browser...will > look back through emails and try to find > what Mary said- bingo- found the introd dvd cited in Mary's earlier email- > have been listening but going to sleep now- > like that words and arrows and "print screen" are included- the arrow helps- > when I suggested you all publish something > to help the naive- this is it and Mary told me, but I didn't begin reading > until now- about 2 wks ago when I first googled > ucsc genome, I hit one of the main (confusing/busy pages)- would have been > useful to see the introd dvd listed (it might > have been but the first page was so busy that I didn't notice...anyway...i > will examine tomorrow...and remain grateful > if anyone has time to help me troubleshoot- i pasted the error message which > so far is meaningless to me > > ((i hope before you post all my emails on your website that you eliminate > extraneous/redundant- one reason I wrote > so many details was to help you track how a naive/interested/fairlysmart > person finds her way through all the words- > tough- what helped the most was Mary's email citing all the webpage introd > dvds etc > A > > On Thu, Mar 31, 2011 at 9:35 PM, Ann Eileen Miller Baker < > [email protected]> wrote: > > >> 1. the below message makes no sense to me >> 2. i am examining the USER MANUAL now, but it is LONNNNNG >> 3. Mary, perhaps when you help someone so much (you laid/layed out all the >> steps), also mention what >> sections of the manual are the most important >> 4. this is already a very useful website and I hope you all take my >> suggestions as you all are >> helping me and I am trying to help you improve what is already a useful >> resource >> >> On Thu, Mar 31, 2011 at 9:31 PM, Ann Eileen Miller Baker < >> [email protected]> wrote: >> >> >>> Can't start query: >>> select >>> tStart,tEnd,qName,0,strand,tStart,tEnd,blockCount,blockSizes,tStarts,tSize >>> from all_sts_primer where tName='chr1' and ((%DMit%)) >>> >>> --------------------------------------------------------------------------- >>> --------------------------------------------------------------------------- >>> mySQL error 1064: You have an error in your SQL syntax; check the manual >>> that corresponds to your MySQL server version for the right syntax to use >>> near '%DMit%))' at line 1 >>> --------------------------------------------------------------------------- >>> >>> >>> >>> >>> >>> above is my error message - I got thrown by rexon which I should have >>> recognized as UTR exon...but anyway, Mary your >>> directions were fairly clear- only the submit is what threw me until my >>> husband suggested--- now what to do about error message >>> >>> QC for you all to think about >>> 1. not so bad >>> 2. since going back to first page is just mechanical but do zip there, >>> perhaps could be >>> eliminated? >>> 3. since so many hoops to jump through, maybe allow the last submission to >>> be saved and then the person >>> fixes the goof rather than resubmitting (all those hoops) >>> >>> I will try to figure out..and hope to get output soon >>> Many thanks so far >>> A >>> >>> >>> >>> On Thu, Mar 31, 2011 at 9:24 PM, Ann Eileen Miller Baker < >>> [email protected]> wrote: >>> >>> >>>> 31Mr11 2132 >>>> I called the first one 5'UTRexon >>>> that choice is not listed >>>> i will try clicking on rexon though that isn't what I typed in >>>> >>>> On Thu, Mar 31, 2011 at 9:14 PM, Ann Eileen Miller Baker < >>>> [email protected]> wrote: >>>> >>>> >>>>> 31Mr11 2112 >>>>> 1. I entered 5'UTRexon and hit the button for 5'UTRexon >>>>> 2. this caused the computer to go back to page 1 >>>>> >>>>> On Thu, Mar 31, 2011 at 9:08 PM, Ann Eileen Miller Baker < >>>>> [email protected]> wrote: >>>>> >>>>> >>>>>> 31Mr31 2107 >>>>>> 1. there is no phrase "submit" on page one- I looked 5X; my husband >>>>>> looked 2X >>>>>> 2. my husband suggested "get output" which led me to next page- is this >>>>>> correct? >>>>>> >>>>>> On Thu, Mar 31, 2011 at 8:50 PM, Ann Eileen Miller Baker < >>>>>> [email protected]> wrote: >>>>>> >>>>>> >>>>>>> 31Mr31 2048 (will work some more; then return here ca. 1500) (thanks >>>>>>> to all for your continuing help/patience) >>>>>>> (I still feel the PRINT SCREEN combined with arrows would help naive >>>>>>> to find places on the fairly busy web page) >>>>>>> >>>>>>> Vanessa and Mary, >>>>>>> 1. I see why on page one I submitted that sequence (see near bottom of >>>>>>> page) >>>>>>> 2. I am reading Mary's directions for me and see NO PLACE ON PAGE ONE >>>>>>> where there is a place >>>>>>> to click submit >>>>>>> A >>>>>>> >>>>>>> >>>>>>> On Thu, Mar 31, 2011 at 6:08 PM, Ann Eileen Miller Baker < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>> >>>>>>>> 31Mr11 1807 >>>>>>>> Vanessa and Mary, >>>>>>>> 1. thnx for fast turnaround >>>>>>>> 2. Mary (if I understood her) said that those DMit markers >>>>>>>> (attached) were part of the UCSC database >>>>>>>> 3. the instructions I read said upload- I will reread what Mary wrote >>>>>>>> and try again >>>>>>>> 4. recall that we need bulk upload/downloads because I have ca. 7500 >>>>>>>> DMit loci. >>>>>>>> 5. I just got back from my EXCEL/ACCESS tutorial and will be >>>>>>>> rereading Mary's directions and then retrying >>>>>>>> 6. note each Friday, I am busy until ca. 1500 (EXCEL class) >>>>>>>> Respectfully, >>>>>>>> A >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Mar 31, 2011 at 5:21 PM, Vanessa Kirkup Swing < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>> >>>>>>>>> Hi Ann, >>>>>>>>> >>>>>>>>> Are you trying to use DMit markers that aren't on the UCSC Genome >>>>>>>>> Browser? The instructions below do not ask you to upload a file. Were >>>>>>>>> you >>>>>>>>> trying to upload a file? >>>>>>>>> >>>>>>>>> Vanessa Kirkup Swing >>>>>>>>> UCSC Genome Bioinformatics Group >>>>>>>>> >>>>>>>>> ----- Original Message ----- >>>>>>>>> From: "Ann Eileen Miller Baker" <[email protected]> >>>>>>>>> To: "Mary Goldman" <[email protected]>, [email protected] >>>>>>>>> Sent: Thursday, March 31, 2011 12:35:45 PM >>>>>>>>> Subject: Re: [Genome] Fwd: pls reply to [email protected] >>>>>>>>> >>>>>>>>> 31Mr 1235 >>>>>>>>> Mary, >>>>>>>>> >>>>>>>>> 1. I submitted the attached (Witmer DMit for ucsc) >>>>>>>>> and got error message >>>>>>>>> >>>>>>>>> hashMustFindVal: 'hgta_pastedIdentifiers' not found >>>>>>>>> >>>>>>>>> 2. this was step directly after custom output >>>>>>>>> >>>>>>>>> 3. I will be here Th until ca. 1500 and return ca. 1700; Friday >>>>>>>>> I am in Eureka for ACCESS/EXCEL classes until ca. >>>>>>>>> 1500- on most days I am here most of time, just not this Th >>>>>>>>> and F >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> A >>>>>>>>> (I am reading your instructions as I try what you say; i.e., I >>>>>>>>> stopped >>>>>>>>> reading when I got error message) >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, Mar 29, 2011 at 4:01 PM, Mary Goldman <[email protected]> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hi Ann, >>>>>>>>>> >>>>>>>>>> I looked at your file and it appears to be a FASTA file of all the >>>>>>>>>> >>>>>>>>> records >>>>>>>>> >>>>>>>>>> from the all_sts_primer table from the mm9 assembly that have >>>>>>>>>> >>>>>>>>> "D1MIT" in the >>>>>>>>> >>>>>>>>>> name. >>>>>>>>>> >>>>>>>>>> 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 "submit". 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. >>>>>>>>>> >>>>>>>>>> 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 "%D1MIT%". 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" and click "submit" >>>>>>>>>> >>>>>>>>>> output format: BED - browser extensible data >>>>>>>>>> >>>>>>>>>> and click "get output". >>>>>>>>>> >>>>>>>>>> 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 3/28/11 6:51 PM, Ann Eileen Miller Baker wrote: >>>>>>>>>> >>>>>>>>>> 28Mr11 >>>>>>>>>> >>>>>>>>>> Mary Goldman, >>>>>>>>>> Thanks for more details, trying to help me learn enough to >>>>>>>>>> find the info I seek. I don't keep the correct email and >>>>>>>>>> would be grateful if you forwarded this email to them or whenever >>>>>>>>>> you respond you include the correct email and I will forward. >>>>>>>>>> Email is fine: I suggested phone because I thought it would >>>>>>>>>> be faster. I guess that recombination rates might be guestimated >>>>>>>>>> (to an order of magnitude?) with recombinant inbred lines. Any >>>>>>>>>> other (indirect way) to guestimate recombination rates >>>>>>>>>> >>>>>>>>> appreciated. >>>>>>>>> >>>>>>>>>> (1a) let me be clearer- the main data I am looking for is >>>>>>>>>> ""where mouse usat (microsatellite loci DMit) are located relative >>>>>>>>>> to ((regulatory genes (promoters, 5' UTR, intergenes etc and >>>>>>>>>> genes (exons)))"" >>>>>>>>>> (1b) in brief, I wish to do for mouse usat DMit what Payseur >>>>>>>>>> (attachment) did for human usat >>>>>>>>>> (2) I have no colleague who refers me to UCSC data on location of >>>>>>>>>> usats (microsatellite loci) with respect to regulatory genes >>>>>>>>>> (3) I know you are trying to do your best to help me, but can >>>>>>>>>> you suggest where I might look to find this information as a file >>>>>>>>>> (rather than entering each of the >> 7500 usat individually) >>>>>>>>>> (4) I will be looking at wikipedia and the helix websites you >>>>>>>>>> suggested asap (in middle of some analyses now, yet wanted >>>>>>>>>> to answer your comments, questions as much as I could. >>>>>>>>>> (5) How I would like to see output: I WANT TO SEE ALL >>>>>>>>>> because I don't know which DMit locus is in exons, introns etc: >>>>>>>>>> (5a) DMit locus name >>>>>>>>>> (5b) is the DMit locus in an >>>>>>>>>> (5b1) exon? >>>>>>>>>> (5b2) coding exon? >>>>>>>>>> (5b3) intron >>>>>>>>>> (5b4) intergene >>>>>>>>>> (5b5) 5'UTR (most likely regulatory gene location) >>>>>>>>>> (5b6) 3'UTR >>>>>>>>>> (5b7) I don't know what cds are (coding?) but will look up in >>>>>>>>>> wikipedia/google >>>>>>>>>> (5c) These output columns could be summarized as "no evidence >>>>>>>>>> for selection (introns)" versus " strong evidence for selection >>>>>>>>>> >>>>>>>>> (exons >>>>>>>>> >>>>>>>>>> in genes important for survival; this would include key promoters >>>>>>>>>> >>>>>>>>> too)" >>>>>>>>> >>>>>>>>>> (6) I have DMit amplified sequences that a colleague sent me >>>>>>>>>> (attached)- the DMit name is embedded within a string of other >>>>>>>>>> info >>>>>>>>>> >>>>>>>>>> Mnay thanks for trying to help- we make progress; I will read what >>>>>>>>>> you suggested asap. Payseur's paragraph in the MatMeth explains >>>>>>>>>> probably more clearly than I can now (still learning). >>>>>>>>>> >>>>>>>>>> Look forward to hearing from you; will send on to correct email; >>>>>>>>>> may write more after reading what you suggested. >>>>>>>>>> >>>>>>>>>> Ann >>>>>>>>>> >>>>>>>>>> On Mon, Mar 28, 2011 at 4:55 PM, Mary Goldman <[email protected]> >>>>>>>>>> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>>> Hi Ann, >>>>>>>>>>> >>>>>>>>>>> I'm sorry but I've looked again and I can't find data on DMits >>>>>>>>>>> >>>>>>>>> here. >>>>>>>>> >>>>>>>>>>> Perhaps your colleague knows which track he used to obtain the >>>>>>>>>>> >>>>>>>>> data from >>>>>>>>> >>>>>>>>>>> UCSC? >>>>>>>>>>> >>>>>>>>>>> To better help you there are a couple of things that need to be >>>>>>>>>>> >>>>>>>>> clarified: >>>>>>>>> >>>>>>>>>>> 1. Do you have genomic coordinates or sequences? If you are >>>>>>>>>>> >>>>>>>>> unsure send a >>>>>>>>> >>>>>>>>>>> small sample in your reply. >>>>>>>>>>> 2. Specify exactly what loci types are you looking for >>>>>>>>>>> >>>>>>>>> (intergenic, 3' >>>>>>>>> >>>>>>>>>>> UTR, CDS, intron or 5'UTR)?. Please note that there is no >>>>>>>>>>> >>>>>>>>> recombination rate >>>>>>>>> >>>>>>>>>>> data available for mouse. >>>>>>>>>>> 3. What are your desired output columns? I'm not sure, but I >>>>>>>>>>> >>>>>>>>> think they >>>>>>>>> >>>>>>>>>>> are DMit locus name, DMit sequence and locus type >>>>>>>>>>> >>>>>>>>> (intron/exon/etc). >>>>>>>>> >>>>>>>>>>> Before you reply, I highly recommend watching both OpenHelix >>>>>>>>>>> >>>>>>>>> tutorials >>>>>>>>> >>>>>>>>>>> below (the first one is about the Genome Browser generally, while >>>>>>>>>>> >>>>>>>>> the second >>>>>>>>> >>>>>>>>>>> one focuses on Custom Tracks and the Table Browser, both of which >>>>>>>>>>> >>>>>>>>> are >>>>>>>>> >>>>>>>>>>> software features that you will be using): >>>>>>>>>>> http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml >>>>>>>>>>> http://www.openhelix.com//cgi/tutorialInfo.cgi?id=28 >>>>>>>>>>> >>>>>>>>>>> Additionally, this Wikipedia article may help you understand what >>>>>>>>>>> >>>>>>>>> we mean >>>>>>>>> >>>>>>>>>>> by "assembly" here at the Genome Browser: >>>>>>>>>>> http://en.wikipedia.org/wiki/Genome_project. In particular, this >>>>>>>>>>> >>>>>>>>> section >>>>>>>>> >>>>>>>>>>> should help make it clear why there are several assemblies for >>>>>>>>>>> >>>>>>>>> each >>>>>>>>> >>>>>>>>>>> organism: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> http://en.wikipedia.org/wiki/Genome_project#When_is_a_genome_project_finished.3F >>>>>>>>> >>>>>>>>>>> . >>>>>>>>>>> >>>>>>>>>>> Finally, I'm very sorry but we are not funded to provide help via >>>>>>>>>>> >>>>>>>>> phone. >>>>>>>>> >>>>>>>>>>> Please reply to the mailing list with any further replies and >>>>>>>>>>> >>>>>>>>> questions. >>>>>>>>> >>>>>>>>>>> Best, >>>>>>>>>>> >>>>>>>>>>> Mary >>>>>>>>>>> ------------------ >>>>>>>>>>> Mary Goldman >>>>>>>>>>> UCSC Bioinformatics Group >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 3/22/11 6:14 PM, Ann Eileen Miller Baker wrote: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> ---------- Forwarded message ---------- >>>>>>>>>>>> From: Ann Eileen Miller Baker<[email protected]> >>>>>>>>>>>> Date: Tue, Mar 22, 2011 at 2:19 PM >>>>>>>>>>>> Subject: Re: [Genome] pls reply to [email protected] >>>>>>>>>>>> To: Vanessa Kirkup Swing<[email protected]> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> 22Mr11 >>>>>>>>>>>> Dr. Kirkup Swing, >>>>>>>>>>>> 0. I am asking for more info because now I am reading a study >>>>>>>>>>>> >>>>>>>>> paralleling >>>>>>>>> >>>>>>>>>>>> my work for which the author made further distinctions than what >>>>>>>>>>>> >>>>>>>>> I >>>>>>>>> >>>>>>>>>>>> originally requested >>>>>>>>>>>> 1. thnx- the original DMit amplified sequences came from JAX >>>>>>>>>>>> >>>>>>>>> Informatics; >>>>>>>>> >>>>>>>>>>>> a colleague sent me the updated sequences which he cited as >>>>>>>>>>>> coming from UCSC- so your sending me back to JAX (now >>>>>>>>>>>> >>>>>>>>> reproduction >>>>>>>>> >>>>>>>>>>>> not informatics) seems odd, but I am willing to try to follow >>>>>>>>>>>> >>>>>>>>> your >>>>>>>>> >>>>>>>>>>>> suggestions >>>>>>>>>>>> once you respond to my more detailed objectives (below, >>>>>>>>>>>> >>>>>>>>> including ## >>>>>>>>> >>>>>>>>>>>> annotations within your helpful suggestions## >>>>>>>>>>>> 2. let me try to be clearer >>>>>>>>>>>> 3. i have ca. 7500 DMit loci (amplified sequences) for usats >>>>>>>>>>>> (microsatellites) making it logistically difficult to handle one >>>>>>>>>>>> >>>>>>>>> locus at >>>>>>>>> >>>>>>>>>>>> a >>>>>>>>>>>> time, which I think >>>>>>>>>>>> you imply below (these DMit amplification sequences are in your >>>>>>>>>>>> ucsc mouse DMit usat archive if I understand my colleague) >>>>>>>>>>>> 4. i am looking for excel files that would have for all DMit >>>>>>>>>>>> >>>>>>>>> usat loci >>>>>>>>> >>>>>>>>>>>> the location of the amplified loci with respect to the >>>>>>>>>>>> >>>>>>>>> following; i.e., >>>>>>>>> >>>>>>>>>>>> which >>>>>>>>>>>> DMit usat loci are in introns? coding exons? etc): >>>>>>>>>>>> 4a. intron >>>>>>>>>>>> 4b. exon versus coding exons >>>>>>>>>>>> 4c. intergenic >>>>>>>>>>>> 4d. 3' and 5' UTR >>>>>>>>>>>> 4e. upstream from transcription start site >>>>>>>>>>>> 5. is there some way to do a "bulk submission" of all these DMit >>>>>>>>>>>> loci rather than piecemeal (one at a time as I think you imply)? >>>>>>>>>>>> Ann >>>>>>>>>>>> ## see below because I don't know what to list for what you >>>>>>>>>>>> state I need to submit >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Mar 21, 2011 at 3:50 PM, Vanessa Kirkup Swing >>>>>>>>>>>> <[email protected]>wrote: >>>>>>>>>>>> >>>>>>>>>>>> Hi Ann, >>>>>>>>>>>> >>>>>>>>>>>>> Sorry for the delayed response. We suggest you try contacting >>>>>>>>>>>>> >>>>>>>>> the >>>>>>>>> >>>>>>>>>>>>> mailing >>>>>>>>>>>>> list (http://reproductivegenomics.jax.org/mailing_list.html) >>>>>>>>>>>>> >>>>>>>>> at the >>>>>>>>> >>>>>>>>>>>>> Jackson Laboratory to see if you can obtain the sequences and >>>>>>>>>>>>> >>>>>>>>> positions >>>>>>>>> >>>>>>>>>>>>> from >>>>>>>>>>>>> for the DMit microsatellite markers. >>>>>>>>>>>>> >>>>>>>>>>>>> Once you have those, go to the main page on our site. Click on >>>>>>>>>>>>> >>>>>>>>> "Tables" >>>>>>>>> >>>>>>>>>>>>> from the blue navigation bar to get to our table browser. >>>>>>>>>>>>> >>>>>>>>>>>>> Set the clade, genome, and assembly. >>>>>>>>>>>>> >>>>>>>>>>>>> ## what goes into clade? I assume genome implies Mus musculus >>>>>>>>>>>>> >>>>>>>>>>>> domesticus; >>>>>>>>>>>> i don't know what assembly means >>>>>>>>>>>> ## I need the output to come in excel or text delimited files >>>>>>>>>>>> >>>>>>>>> because I >>>>>>>>> >>>>>>>>>>>> do >>>>>>>>>>>> the >>>>>>>>>>>> analyses in EXCEL and in ACCESS; i.e., these formats require a >>>>>>>>>>>> "dedicated" >>>>>>>>>>>> column for each kind of data >>>>>>>>>>>> ## my colleague sent me the DMit amplified sequences in FASTA >>>>>>>>>>>> >>>>>>>>> format; >>>>>>>>> >>>>>>>>>>>> however, since the amplified sequence, has no regular >>>>>>>>>>>> >>>>>>>>> (predictable) >>>>>>>>> >>>>>>>>>>>> structure, >>>>>>>>>>>> there is no way to program to get data into "dedicated columns"; >>>>>>>>>>>> >>>>>>>>> i.e., >>>>>>>>> >>>>>>>>>>>> colA >>>>>>>>>>>> DMit >>>>>>>>>>>> locus name; colB amplified sequence >>>>>>>>>>>> >>>>>>>>>>>> ## may I be sent your phone# so I can try calling if you fail to >>>>>>>>>>>> understand >>>>>>>>>>>> this? I am usually at 707 786 5342 except for Fridays; this week >>>>>>>>>>>> >>>>>>>>> has an >>>>>>>>> >>>>>>>>>>>> unpredictable schedule because it is partly a vacation week; >>>>>>>>>>>> >>>>>>>>> otherwise >>>>>>>>> >>>>>>>>>>>> that >>>>>>>>>>>> phone I will answer >>>>>>>>>>>> >>>>>>>>>>>> Set the following: >>>>>>>>>>>> >>>>>>>>>>>>> track: "UCSC Genes" >>>>>>>>>>>>> table: "knownGene" >>>>>>>>>>>>> >>>>>>>>>>>>> ### >>>>>>>>>>>>> >>>>>>>>>>>> ((this is where we need to have bulk submission since I have >>>>>>>>>>>> >>>>>>>>> ca. 7500 >>>>>>>>> >>>>>>>>>>>> DMit >>>>>>>>>>>> >>>>>>>>>>>> region: "position" and click on "define regions." Paste your >>>>>>>>>>>> >>>>>>>>> regions in >>>>>>>>> >>>>>>>>>>>>> the >>>>>>>>>>>>> box and click "submit" >>>>>>>>>>>>> output format: "all fields from selected table" >>>>>>>>>>>>> >>>>>>>>>>>>> click "get output" >>>>>>>>>>>>> >>>>>>>>>>>>> ## sorry but I am not good at making deductions unless I know >>>>>>>>>>>>> >>>>>>>>> well what >>>>>>>>> >>>>>>>>>>>> I am doing >>>>>>>>>>>> >>>>>>>>>>>> exon= expressed gene >>>>>>>>>>>> intron= where the boundary of the exon is; the intron is outside >>>>>>>>>>>> >>>>>>>>> the exon >>>>>>>>> >>>>>>>>>>>> boundary >>>>>>>>>>>> >>>>>>>>>>>> ## given what I wrote above, how can the pcr silico be of use? >>>>>>>>>>>> >>>>>>>>>>>> The result is the record for your gene. The exon/intron >>>>>>>>>>>> >>>>>>>>> boundaries can be >>>>>>>>> >>>>>>>>>>>>> deduced from the exonStarts and exonEnds fields. If there are >>>>>>>>>>>>> >>>>>>>>> many >>>>>>>>> >>>>>>>>>>>>> fields in >>>>>>>>>>>>> the record that you don't need, you can hit the back button and >>>>>>>>>>>>> >>>>>>>>> change >>>>>>>>> >>>>>>>>>>>>> the >>>>>>>>>>>>> output format to "selected fields from primary and related >>>>>>>>>>>>> >>>>>>>>> tables." >>>>>>>>> >>>>>>>>>>>>> Click >>>>>>>>>>>>> "get output" and select the fields you wish to see in your >>>>>>>>>>>>> >>>>>>>>> results, be >>>>>>>>> >>>>>>>>>>>>> sure >>>>>>>>>>>>> to include exonStarts and exonEnds since these fields contain >>>>>>>>>>>>> >>>>>>>>> the data >>>>>>>>> >>>>>>>>>>>>> you >>>>>>>>>>>>> asked about. >>>>>>>>>>>>> >>>>>>>>>>>>> Also, you may be interested in UCSC In-Silico PCR for mapping >>>>>>>>>>>>> >>>>>>>>> PCR >>>>>>>>> >>>>>>>>>>>>> products. >>>>>>>>>>>>> To get to it, click on "PCR" from the blue navigation bar. >>>>>>>>>>>>> >>>>>>>>>>>>> Hope this helps! If you have further questions related to the >>>>>>>>>>>>> >>>>>>>>> Genome >>>>>>>>> >>>>>>>>>>>>> Browser, please contact the mailing list. >>>>>>>>>>>>> >>>>>>>>>>>>> ## we are further along, but I want to hold off trying to use >>>>>>>>>>>>> >>>>>>>>> UCSC >>>>>>>>> >>>>>>>>>>>> (which I >>>>>>>>>>>> tried >>>>>>>>>>>> w/o help and got nowhere) but I think you are only giving me >>>>>>>>>>>> - intron >>>>>>>>>>>> - exon >>>>>>>>>>>> whereas I also need >>>>>>>>>>>> - recombination hotspots >>>>>>>>>>>> - coding exon versus noncoding exon >>>>>>>>>>>> - 3' and 5' UTR >>>>>>>>>>>> - intergenic >>>>>>>>>>>> >>>>>>>>>>>> Vanessa Kirkup Swing >>>>>>>>>>>> >>>>>>>>>>>>> UCSC Genome Bioinformatics Group >>>>>>>>>>>>> >>>>>>>>>>>>> ----- Original Message ----- >>>>>>>>>>>>> From: "Ann Eileen Miller Baker"<[email protected]> >>>>>>>>>>>>> To: [email protected] >>>>>>>>>>>>> Sent: Wednesday, March 16, 2011 7:53:57 PM >>>>>>>>>>>>> Subject: [Genome] pls reply to [email protected] >>>>>>>>>>>>> >>>>>>>>>>>>> pls reply to [email protected] because I am unclear how >>>>>>>>>>>>> >>>>>>>>> to >>>>>>>>> >>>>>>>>>>>>> access >>>>>>>>>>>>> the >>>>>>>>>>>>> normal channel where replies are put >>>>>>>>>>>>> >>>>>>>>>>>>> (1) How can I find mouse DMit (microsatellite loci) amplified >>>>>>>>>>>>> >>>>>>>>> sequences? >>>>>>>>> >>>>>>>>>>>>> (url) >>>>>>>>>>>>> (2) alleles at inbred strains for DMit microsatellite loci? >>>>>>>>>>>>> >>>>>>>>> (url) >>>>>>>>> >>>>>>>>>>>>> (3) How can I find which DMit microsatellite loci are in >>>>>>>>>>>>> - introns >>>>>>>>>>>>> - exons >>>>>>>>>>>>> - recombination hot spots >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> 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 >>>>>>>>> >>>>>>>>> >>>>>>>> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
