Hello, The only problem I see with this approach is that Alt Events data represent exons changes that appear less often than the majority. If you exclude transcripts with these regions by base overlap, you will miss well represented exons.
For example: In the latest human, hg18 Set tracks UCSC Genes, Alt Events, CCDS, and RefSeq Genes to pack, turn everything else on to hide. Set position/search to chr21:9,934,842-9,941,996 This feature in the Alt Events track represents a single transcript that is missing the exon. Item: cassetteExon Position: chr21:9938241-9938346 The majority of transcripts do have the exon. So excluding transcripts that have base overlap with this feature will give you the opposite results than intended. A track like CCDS represents a very conservative set of coding sequences. One relevant line from this track's description page is "This project is a collaborative effort to identify a core set of human protein-coding regions that are consistently annotated and of high quality." Read the complete track description (and links to the contributor's web site) to see if this is useful for you. Also, have you examined the data contained in the "knownCanonical" table? You can find this table in the Table browser under the UCSC Genes track. "Format description: Describes the canonical splice variant of a gene". This may be what you are looking for. If I have misunderstood, please write back with an example and we can work out the details, Jennifer Jackson UCSC Genome Bioinformatics Group ps. knownAlt is the primary table of the Alt Events track, so I am making the assumption that there was a small error in your query description and that you meant that you were going to compare knownGenes with knownAlt by base overlap. Clancy, Kevin wrote: > Dear Sirs > I am interested in identifying constant exons within the Genes and gene > prediction Tracks. I understand that I can find alternative splice exons > within the Alt Events track. And I can find all exons for a given gene > within the UCSC genes track. So if create an intersection with Known Alt > table that has no overlap with Alt Events, I want to confirm that the > result of this would be constant exons that appear in the majority of > transcripts associated with a given gene. > Thanks > kevin > > Kevin Clancy, PhD > Senior Scientist > Informatics & eCommerce > Life Technologies > 5791 Van Allen Way > Carlsbad CA 92008 > phone: 760 268 8356 > cell: 240 417 8604 > email: [email protected] > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
