Ucsc Track Friendly Format For Cds Sequences And Coordinates?

Question

[user]

I want to represent a set of sequences that occur within CDS regions of genes and then load these as UCSC tracks to browser. I need to fetch the CDS sequence of a gene, see where my sequences of interest lie, and then output that as a format loadable in a track in UCSC. What is the right format for this? It would need to represent spliced alignments since CDS coordinates are different from the genomic coordinates. Is there an easy and flexible format to keep all necessary info in?

[Maximilian Haeussler]

I don't understand why you cannot use something like bed or bigBed. Both support "introns". Do you know these formats? Or have you eliminated them for some reason? They both well documented and can be used from customTracks or track hubs.

Answer 1

[Devon Ryan]

Probably BAM or GTF/GFF would be the most convenient. With BAM, you could put the relevant sequences in and show splicing with CIGAR operators.