Hi Dan, If there is more than one exon for a particular transcript, the results for that transcript are ordered by chromStart, but then additional transcripts will not necessarily be sorted relative to one another.
If you need the output to be ordered by position, the UNIX/gnu sort command can do that easily: sort -k1,1 -k2n,2n myFile > mySortedFile Additionally, you should be aware that some non-coding genes are showing up in your results. If you would like to exclude those genes, you can add a filter in the Table Browser. Hit the "filter: create" button, and then in the "Free-form query" box add "cdsStart != cdsEnd" (without the quotes). Genes with no coding region (CDS) appear in our tables with the same number for cdsStart and cdsEnd, so this filter will keep those genes from appearing in the output. We are going to look into changing the options in the Table Browser so that non-coding genes will not appear in the results when the 3'UTR or 5'UTR output types are selected. I hope this information is helpful. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 3/29/12 9:26 PM, Dan Morton wrote: > Hello, > > If I download ETV6 from knownGene table and download the custom track for > 5' UTR I was wondering what the data is sorted by. At first it appeared to > be by the 5'UTR Exon start but with closer inspection this is not the case. > > Here is a snippet from my results: > > chr12 | 11187380 | 11187484 | uc001qzb.4_utr5_8_0_chr12_11187381_r | > 0 | - > chr12 | 11199618 | 11199787 | uc001qzb.4_utr5_9_0_chr12_11199619_r | > 0 | - > chr12 | 11324020 | 11324224 | uc001qzb.4_utr5_10_0_chr12_11324021_r > | 0 | - > chr12 | 10998447 | 10998549 | uc021qve.1_utr5_0_0_chr12_10998448_r | > 0 | - > chr12 | 10999643 | 10999966 | uc021qve.1_utr5_1_0_chr12_10999644_r | > 0 | - > chr12 | 11000970 | 11001006 | uc021qve.1_utr5_2_0_chr12_11000971_r | > 0 | - > > I do not understand the ordering of the results, any information will be > greatly appreciated. > > Thanks, > Dan > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
