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
