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 >>> >> >
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