Hi Luvian, May I have a relevant question that I've downloaded all the coding exons from UCSC table browser which looks like the followings:
chr1 324342 324345 uc009vjk.2_cds_1_0_chr1_324343_f 0 + chr1 324438 325605 uc009vjk.2_cds_2_0_chr1_324439_f 0 + chr1 324342 324345 uc001aau.2_cds_1_0_chr1_324343_f 0 + chr1 324438 325605 uc001aau.2_cds_2_0_chr1_324439_f 0 + chr1 367658 368594 uc010nxu.1_cds_0_0_chr1_367659_f 0 + chr1 621098 622034 uc010nxv.1_cds_0_0_chr1_621099_r 0 - chr1 664484 665108 uc001abe.3_cds_0_0_chr1_664485_r 0 - chr1 664484 665108 uc009vjm.2_cds_0_0_chr1_664485_r 0 - I have some difficulties to understand the 4th column of this file. 1) I presume 'uc*****.*' is the UCSC ids. By looking at the first four records on the genome browser, they seem corresponding to the same gene. Are they alias? 2) What do those numbers following 'cds_' mean? Are they indexing exons of a gene? 3) After 'chr1', the number obviously represents some position information, but I am not sure what position exactly? It looks 1bp after the start position on the 2nd column. I interpret the 2nd & 3rd column as the exon coordinates. Am I wrong? Thank you very much in advance! Yuan On 4 Mar 2011, at 21:11, Luvina Guruvadoo wrote: > Hi Bogdan, > > Please see these two previously answered mailing list questions: > > https://lists.soe.ucsc.edu/pipermail/genome/2010-February/021412.html > > https://lists.soe.ucsc.edu/pipermail/genome/2007-August/014337.html > > If by non-redundant exons you mean that you don't want exons of splice > variants, then you may want to first obtain a list of transcripts from > the knownCanonical table using the Table Browser. To do this, select > "knownCanonical" from the table drop down menu, then "selected fields > from primary related tables" as the output format. Enter a file name > in > the output file box and click "get output". On the following page, > select "transcripts" then "get output". This will provide you with a > file containing all transcript names. Then follow instructions on the > previous mailing list questions to obtain the exons, with the > additional > step of uploading the list of transcripts (click "upload list" next to > identifiers). > > I hope this helps. Please contact us again at [email protected] if > you > have any further questions. > > Best, > Luvina > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > > > Bogdan Tanasa wrote: >> Dear all, >> >> please could you let me know a way to retrieve the non-redundant >> set of >> exons of UCSC genes of hg18. >> >> thanks, >> >> bogdan >> _______________________________________________ >> 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
