Hi David, Wait, I'm not sure I understand what you are doing. How did you create the "rna_exons" custom track? Does *that* track have intron/exon structure? If not, then you will not be able to get sequence corresponding to exons back.
If so, if you have that track selected in the Table Browser, and you have created an intersection with your my_regions track with "All rna_exons records that have any overlap with my_regions," and then you choose "output format: sequence" (and be sure to deselect "introns" on the sequence retrieval options), you *should* get only exons back, and the names should be retained. I tried it with a small sample and it worked. I'm thinking that either your rna_exons track somehow lost the intron/exon structure and is just a simple BED with only the first 4 fields, or that you didn't notice that you need to deselect "introns" on the sequence retrieval page. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/22/11 12:56 PM, Managadze, David (NIH/NLM/NCBI) [F] wrote: > Thanks for suggestions, Brooke. > > You are right: "All rna_exons records that have any overlap with > my_regions" will give me not only exons but whole genomic sequence. > > It is a funny coincidence that I have been trying to do this on > Galaxy all day long. The Galaxy has some problems today. > > I will keep trying :) > > Thanks again, > > David > > On Dec 22, 2011, at 3:50 PM, Brooke Rhead wrote: > >> Hi David, >> >> You are correct: the Table Browser will discard the names of your >> custom track items and produce a simple list of position ranges if >> one of the base-pair-wise options is chosen. >> >> If you choose one of the intersection options to get, for instance, >> "All rna_exons records that have any overlap with my_regions," the >> rna_exons names will be retained. However, that might not be what >> you want! >> >> This is a known limitation of the Table Browser (and something we >> would like to improve in the future). In the meantime, there is >> another tool, Galaxy, which is run by Penn State and works in >> conjunction with the Table Browser: >> >> http://main.g2.bx.psu.edu/ >> >> I suggest looking at the tools listed under the "Operate on >> Genomic Intervals" and "Join, Subtract and Group" headers. If you >> have any questions on using Galaxy, please contact their helpdesk >> at [email protected]. >> >> -- Brooke Rhead UCSC Genome Bioinformatics Group >> >> >> >> On 12/22/11 7:45 AM, Managadze, David (NIH/NLM/NCBI) [F] wrote: >>> Thanks for the suggestion. >>> >>> I did base-pair-wise intersection (AND) of my_regions vs >>> rna_exons and vice versa. >>> >>> In both cases, I get the sequences(or intervals) of intersected >>> exons but MY ID INFORMATION IS LOST! >>> >>> For instance, if there was one ID of my_regions from chrX >>> containing 5 exons, 2 of which overlapped, I got 4 entries with >>> IDs: chrX.1, chrX.2, chrX.3 and chrX.4 One of these represented >>> those two exons merged into one. >>> >>> David >>> >>> >>> On Dec 21, 2011, at 6:01 PM, Vanessa Kirkup Swing wrote: >>> >>>> Hi David, >>>> >>>> We recommend that that if you want whole rna exons, you will >>>> need to start by selecting the other track, rna_exons, first in >>>> the table browser, then do the intersection. If you want want >>>> a base-pair-wise intersection, you can choose the >>>> "Base-pair-wise intersection (AND)" option when creating an >>>> intersection in the table browser. >>>> >>>> If you have further questions, please email the list: >>>> [email protected]. >>>> >>>> Vanessa Kirkup Swing UCSC Genome Bioinformatics Group >>>> >>>> >>>> >>>> ---------- Forwarded message ---------- From: Managadze, David >>>> (NIH/NLM/NCBI) [F]<[email protected]> Date: Tue, Dec >>>> 20, 2011 at 1:51 PM Subject: [Genome] Get concatenated exon >>>> sequences of my regions spanning several genes To: >>>> "[email protected]"<[email protected]> >>>> >>>> >>>> I have certain regions of mm9 track. (And I also know that >>>> there are one or more ncRNA genes in these regions) >>>> >>>> I would like to get the concatenated sequences of all exons >>>> corresponding to each of my region as one fasta record. >>>> >>>> Could you please suggest the way? >>>> >>>> I tried to create two tracks: my_regions and rna_exons Then I >>>> tried to get the sequence of my_regions that intersect with >>>> rna_exons track. The browser still returns the whole my_regions >>>> and not just exons because it returns the whole of my_regions >>>> that intersect with exons, not just exon parts. (which perhaps >>>> is logical but still...) >>>> >>>> Thanks in advance for your help. >>>> >>>> David _______________________________________________ Genome >>>> maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >>> >>> _______________________________________________ Genome maillist >>> - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome > y _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
