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
