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> >> >
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