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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
