Hi Alexander, I'm not completely sure what you're trying to do. If you want to intersect only cdsStart and cdsEnd (not txStart/txEnd, nor the blocks) with some other table, then you can try using selected fields to get only those coordinates, and then rearrange the columns to get BED4 (or if you need BED6, rearrange and add a dummy score column with 0's). Then upload that as a custom track and do the intersection.
If that's not what you're asking, Galaxy (http://main.g2.bx.psu.edu/) or BEDtools (http://code.google.com/p/bedtools/) might have a solution. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 11/2/11 1:08 AM, Alexander Belostotsky wrote: > Thank you very much! > > As far as I understand from your letter, Table Browser searches for > intersection between all blocks by default. It is what I really need. > But as a result I obtain intersection between pos_left and pos_right > of some table and ONLY CDS of knowngene. I checked this out. > > So could you just tell me how can I see intersections between some > table pos_left and pos_right and txStart and txEnd of knowngene by > using Table Browser. > > Thank you! > Alexander > > 2011/11/1 Greg Roe <[email protected] <mailto:[email protected]>> > > Hi Alexander, > > One of our engineers commented: > " When a table has block structure (e.g., exons in genePred or > bed, gapless aligned blocks in psl), the Table Browser intersects > only the blocks instead of the entire span... and all blocks, not > just the CDS portion. Unless the primary table is a wiggle... that > does the entire span of the secondary table items regardless of > block structure! Of course it would be nicer to offer the option > of whole span or blocks (or CDS when known), but I don't know of > any plans to add that functionality." > > Please let us know if you have any additional questions: > [email protected] <mailto:[email protected]> > > - > Greg Roe > UCSC Genome Bioinformatics Group > > > On 10/31/11 5:21 AM, Alexander Belostotsky wrote: >> Hello, dear members of glorious UCSC Genome Browser team :) , >> >> I think it would be nice to report that *results of intersection between >> some table and "knowngene" table in Table Browser give results of >> intersection between this table and CDS coordinates in "knowngene" >> table.* >> At least this occurs in hg18 assembly. >> I suppose that people who use this want to have intersection between some >> table and TX coordinates. So, it should be intersection between some let >> say (pos_left between txStart and txEnd) and (pos_right between txStart >> and >> txEnd). >> >> Am I right. If you think yes, please settle the problem. >> >> Best wishes, >> Alexander >> _______________________________________________ >> Genome maillist [email protected] <mailto:[email protected]> >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
