Hi Brent, Regarding this part of your original email:
> chrom,txStart,txEnd,cdsStart,cdsEnd,K.name,X.geneSymbol,proteinID,strand,exonStarts,exonEnds > from knownGene as K,kgXref as X where X.kgId=K.name ... > I have seen this: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 so the > internal format matches the BED format, correct? Actually, those columns are from an internal format that we call genePred. BED has a bit different column order, and it has a very different encoding of block coordinates: instead of lists of starts and ends like genePred, BED has a list of block sizes followed by a list of block starts -- but each block start is relative to the overall chromStart (analogous to genePred's txStart), so block starts always begin at 0. The Table Browser has BED as one of its output formats, so it's the easiest way to get BED for a genePred table (or just about any non-BED table that has chrom, start, end and other fields). Hope that helps, Angie _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
