---------- Forwarded message ---------- From: Maximilian Haussler <[email protected]> Date: Mon, May 24, 2010 at 8:09 PM Subject: Re: [Genome] Intergenic Regions in Human Genome To: Peter Cote <[email protected]>
I think I know where your problem was: first, do the "intersection" (actually: a union) of the two tracks with OR and do NOT invert them yet. Create a new custom track using this called "union". Then goto the table browser again, select the "union" track, intersect it with itself, operation is "OR". Now select the two inversion checkboxes. create a new track "intergenic". Here is what I got: http://www.genome.ucsc.edu/cgi-bin/hgTracks?hgsid=160605701&db=hg18 does this work for you? cheers Max On Mon, May 24, 2010 at 7:54 PM, Peter Cote <[email protected]> wrote: > Is this the link you mean? Sorry it took so long > > > http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=160581632&hgta_ctName=tb_ct_intergenicregions&hgta_ctDesc=complement+of+intron+and+exon+table&hgta_ctVis=dense&hgta_ctUrl=&fbQual=whole&fbUpBases=200&fbDownBases=200&hgta_doGetCustomTrackFile=get+custom+track+in+file > > > On Mon, May 24, 2010 at 8:03 PM, Maximilian Haussler < > [email protected]> wrote: > >> I have the impression that this method should work. Noteably, it shold >> produce a custom track with features that start and end at gene boundaries. >> Can you send me a link to your custom track or a little snippet? >> >> >> >> On Mon, May 24, 2010 at 5:54 PM, Peter Cote <[email protected]> wrote: >> >>> I used the Table Browser following the method described here: >>> https://lists.soe.ucsc.edu/pipermail/genome/2007-March/013036.html >>> >>> Thanks for the other link, I'll look at that too. >>> Peter >>> >>> >>> On Mon, May 24, 2010 at 7:38 PM, Maximilian Haussler < >>> [email protected]> wrote: >>> >>>> Hm, which method did you use to obtain the intergenic regions? table >>>> browser? script? >>>> >>>> if you used my script, what was the input file like? >>>> >>>> max >>>> >>>> >>>> >>>> >>>> On Mon, May 24, 2010 at 5:34 PM, Peter Cote <[email protected]> wrote: >>>> >>>>> Thanks! >>>>> >>>>> I was able to obtain the intergenic regions. I was looking at the data >>>>> for the intergenic regions and I was comparing it to the knownGenes table, >>>>> I'm not sure if my understanding of intergenic regions is correct but I >>>>> thought that where every intergenic region ends, a gene should begin and >>>>> vice versa. That doesn't look like the case. Do you know why this is? >>>>> >>>>> Also, one of my friends suggested that I "grab the table with contigs" >>>>> to exclude centromeres and telomeres from the data and I can't figure out >>>>> how to do that. Any suggestions? >>>>> >>>>> Thanks for your help! >>>>> >>>>> Peter >>>>> >>>>> >>>>> On Mon, May 24, 2010 at 4:42 PM, Maximilian Haussler < >>>>> [email protected]> wrote: >>>>> >>>>>> Hi Peter, >>>>>> >>>>>> I remember a previous post on this: >>>>>> http://www.mail-archive.com/[email protected]/msg01114.html. The >>>>>> user said that the method presented with the table browser timed out, >>>>>> but it should work now. >>>>>> >>>>>> If you experience other problems or need the flanking genes annotated: >>>>>> I wrote a script some time ago as an alternative, you can give it a >>>>>> try, it >>>>>> might at least be a good starting point (NB: you should use a >>>>>> chromosome.sizes file for this, see help messages): >>>>>> http://max.smith.man.ac.uk/download/scripts/bedBetween.py >>>>>> >>>>>> cheers >>>>>> Max >>>>>> >>>>>> >>>>>> >>>>>> On Mon, May 24, 2010 at 12:56 PM, Peter Cote <[email protected]>wrote: >>>>>> >>>>>>> Hello >>>>>>> >>>>>>> I am trying to obtain the coordinates for the intergenic regions in >>>>>>> the >>>>>>> Human Genome. Using the knownGenes table, on the Table Browser is >>>>>>> there a >>>>>>> way to join the overlapping transcripts and then obtain the >>>>>>> intergenic >>>>>>> intervals between these genes? >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> Peter >>>>>>> _______________________________________________ >>>>>>> Genome maillist - [email protected] >>>>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
