Hello Libia Pava, If you choose the BED output format and click "5' UTR Exons" or "3' UTR Exons" then the strand is taken into account, and the item name indicates whether it is 5' or 3', e.g. this "-" strand refGene (position = chr21:32584947-32932290):
chr21 32639288 32639299 NM_003253_utr5_24_0_chr21_32639289_r 0 - chr21 32649047 32649224 NM_003253_utr5_25_0_chr21_32649048_r 0 - chr21 32711557 32711737 NM_003253_utr5_26_0_chr21_32711558_r 0 - chr21 32836295 32836348 NM_003253_utr5_27_0_chr21_32836296_r 0 - chr21 32931239 32931290 NM_003253_utr5_28_0_chr21_32931240_r 0 - Note that the utr3 results are from chromStart to thickStart and the utr5 results are from thickEnd to chromEnd (of the "whole gene" bed output). If you are using BED output and the UTR Exons options as above but still having trouble please send me an example. If you are wanting "-" strand coords to be reverse complemented you will need to do that locally. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 10/27/10 08:33, Libia Pava wrote: > Hello everyone, > > I was actually having some trouble with the table browsing when it comes to > the different ends of the strand. It seems as if the 5' and 3' ends are not > differentiated when it comes to the table. See, I'm trying to find UT > regions on both sides of the strand, yet I come up with numbers that imply > they are only reading from right to left, or left to right without taking > into account the actual direction of transcription. i know that I can lok at > individual genes to figure out which end it's on, but how can I know where > the UT regions are when I have thousands of base pairs? > > Thanks, > > Libia Pava > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
