Hi Aga, Please try loading the BED file you created (which contains the exon coordinates of your genes of interest) in our UCSC Genes browser. Then compare your custom track to the gene track from which you created your BED file. If you see extra exons in your custom track that you don't see in the original track, please write back to the list so that we can help troubleshoot the creation of your BED file. Here is some information on custom tracks: http://genome.ucsc.edu/goldenPath/help/customTrack.html.
If you don't see any extra exons, then the issue may be with the aligning of your BED file to your downloaded sequence in your visualization tool. If so, I suggest contacting the help resources of the visualization tool your are using for additional assistance. I hope this is helpful. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group A Bierzynska wrote, On 3/4/2011 7:28 AM: > > Dear Technical Support, > > I try to create an annotated refseq which I'll be able to use for > analyzing my next gen seq data. > > Because I'm interested in several hundreds genes I used the UCSC to > create chr coordinates for each exon of each gene which I'm interested > in. The chr coordinates had been used to design probes for capturing > the genes. > > To get the coordinates I uploaded a list of gene symbols and chose BED > as an output format. I had an option to choose number of bp to add at > each side of the exon and I typed 15-so I should get chr coordinates > for all the exons extended for the 15bp at each end (15bp exon 15bp). > > I downloaded sequences and annotations for each of the human > chromosomes(hg19) from UCSC. > > Then I created a gtf file with the coordinates and annotated them on > the refseq. > > I got confused when I saw that the coordinates sometimes are created > not only for the exons.. - I attached few pictures so you can see what > I mean. The coordinates you can see as a pink bars. > Looks like the coordinates are sometimes for exons which doesn't exist... > > Could you please explain me why did it happen and what that is? > Thank you > > Best wishes, > > Aga > ---------------------- > A Bierzynska > Academic Renal Unit > University of Bristol > [email protected] > > > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
