Hi Ann, Instead of trying to copy / paste data from your web browser, try downloading the output directly into a file by entering an output file name. This will start a download of the output data into a file onto your computer.
Also, make sure to re-read the previous instructions to make sure you are entering everything correctly. If you have any additional questions, please reply to: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 12/11/11 12:47 PM, Ann Eileen Miller Baker wrote: > 11Dc11 > Genome Team, > > My objective is finding the first coding exon and first intron. Per > Vanessa's advice, > I went back to TABLE BROWSER and re-extracted coding exons and introns > (attachments) keeping all the UCSC data coming with the DMIT locus. > > Now I try following Brooke's directions (below) but feel stuck. Note that > most > DMIT loci appear once, I assume BUT WOULD LIKE YOU TO CONFIRM that > the first listing of a unique DMIT locus refers to the FIRST (intron or > coding > exon). I do see "_0" or "0" or "0-".. > > In Brooke's directions below, the code "_0" > is the way to recognize the first (intron OR coding exon). In my attached > EXCEL file > for coding exon these data are in col F(0) and col G (-). Note that col G > is a minus > sign not an underline. > > I don't know what it means when col G for coding exon has a "+"- I assume > this > is NOT the first coding exon. > > Note that I see NO > (1) sequence when using the same protocol as used earlier (with earlier > help from Vanessa, Katrina, and others). > (2) uc002yow.1 > > The intron output for Table Browser has the "_0" in columns G. H. L, M : > I don't know which column(s) are my way to recognize first intron. > > Another confusing part is "0" in many places and none with "_0"; instead > "0" or "0_" or "0-". > > Pls help clarify.how I can read the UCSC output to find the first coding > exon or > first intron. Pls use the attached output to help me extract only those > DMIT loci > in the first intron or first coding exon. > > I am a rookie with TABLE BROWSER and interpreting the output, though I > appreciate > Brooke's giving an example with other genes. > > Brooke and Vaness thanks for coaching.Sorry to prolong this. > Looking forward to hearing from you, > Ann > > On Mon, Dec 5, 2011 at 8:43 PM, Brooke Rhead<[email protected]> wrote: > >> Hi Ann, >> >> Yes, you can recognize the first intron and the first coding exon from the >> Table Browser output. >> >> I am looking at the previous answer in this thread to see how you have the >> Table Browser set up: >> https://lists.soe.ucsc.edu/**pipermail/genome/2011-August/**026907.html<https://lists.soe.ucsc.edu/pipermail/genome/2011-August/026907.html> >> If you had the "One FASTA record per region..." selected in the Table >> Browser when you downloaded data, the following should work: >> >> For each gene in your output files, the first (that is, the one on the 5' >> end) intron is simply the first block of sequence listed for that gene in >> your "introns" file. The first coding exon is simply the first exon listed >> for that gene in your "CDS exons" file. >> >> The first intron or coding exon is listed first regardless of the gene >> being on the negative or positive strand. (This is contrary to what >> Katrina said before: "For genes on the - strand, your script will have to >> determine which of the regions has the highest intron/exon number and pull >> that as the first intron or exon." Sorry for the confusion.) >> >> Additionally, there will be a "_0" appended to the first block of sequence >> output for each gene. >> >> So, for example, your intron and exon files should each have several >> blocks of sequence, each beginning with headers (lines that begin with >> ">"), like this: >> >>> hg19_knownGene_uc002yow.1_0 range=chr21:32638326-32639288 5'pad=0 3'pad=0 >> strand=- repeatMasking=none >> (sequence) >>> hg19_knownGene_uc002yow.1_1 range=chr21:32624058-32624505 5'pad=0 3'pad=0 >> strand=- repeatMasking=none >> (sequence) >>> hg19_knownGene_uc002yow.1_2 range=chr21:32617804-32617976 5'pad=0 3'pad=0 >> strand=- repeatMasking=none >> (sequence) >> etc. >> >> The blocks with the same identifier (uc002yow.1) contain sequence for one >> gene. The first intron in that gene (if you are looking at the introns >> file) or exon (if you are looking at the exons file), is the block with the >> "_0" after it, and it is listed first. >> >> I hope this helps explain the output from the Table Browser. If you have >> further questions, please reply to [email protected]. >> >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 12/1/11 6:01 PM, Ann Eileen Miller Baker wrote: >> >>> 1Dc11 >>> Is there a way to RECOGNIZE the FIRST INTRON and FIRST CODING EXON from >>> all >>> output of the TABLE BROWSER? I include the past history of this question >>> in >>> earlier >>> emails (attached; recall this is for ca. 6600 DMIT microsatellite loci >>> discovered by >>> Bill Dietrich and his colleagues - I deduce from Brooke's answer that >>> there >>> is no way to distinguish the first intron from other introns; the first >>> coding exon from other coding exons. >>> Thanks for your help now and in the past, >>> Ann >>> >>> >>> On Thu, Aug 25, 2011 at 1:04 PM, Brooke Rhead<[email protected]> wrote: >>> >>> Hello Ann, >>>> The Table Browser does not have an option to limit output to only the >>>> first intron or first coding exon. >>>> >>>> -- >>>> Brooke Rhead >>>> UCSC Genome Bioinformatics Group >>>> >>>> >>>> >>>> On 08/25/11 10:00, Ann Eileen Miller Baker wrote: >>>> >>>> 25Au11 >>>>> Please answer below. I am aware that the table browser delivers >>>>> for mouse DMIT microsatellite loci overlapping introns, exons, coding >>>>> exons, >>>>> and UTR, but I am asking if there is any way to customize this listing >>>>> to >>>>> include FIRST INTRON; FIRST CODING EXON. >>>>> Thanks, >>>>> Ann >>>>> >>>>> ---------- Forwarded message ---------- >>>>> From: Ann Eileen Miller Baker<[email protected]**> >>>>> Date: Sun, Aug 21, 2011 at 3:45 PM >>>>> Subject: identifying "first intron", "first coding exon" >>>>> To: [email protected] >>>>> >>>>> >>>>> 21Au11 >>>>> Dear UCSC genomics team, >>>>> When determining genomic elements (UTR, exons, coding exons, introns) >>>>> co-occuring with DMIT microsatellite loci, >>>>> <<Is there a way to specify requesting first intron, first coding >>>>> exon>>? >>>>> Thanks, >>>>> Ann >>>>> ______________________________****_________________ >>>>> Genome maillist - [email protected] >>>>> https://lists.soe.ucsc.edu/****mailman/listinfo/genome<https://lists.soe.ucsc.edu/**mailman/listinfo/genome> >>>>> <https:**//lists.soe.ucsc.edu/mailman/**listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>>>> >>>> ______________________________**_________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<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
