mbdebian
commented
6 years ago Is any action going to be taken on this? If not, we should annotate this possible addition somewhere else, in order to keep the repo in sync with the current working iteration of the tool.
To follow-up on the bigGenePred idea:
(http://genome.ucsc.edu/goldenPath/help/bigGenePred.html ) it allows one to translate the underlying reference codon sequence to display. There won't always be a match, I believe, between your real-world experimental MS data and the reference coding AA sequence so if you used our bigGenePred you might have divergence (where the bigGenePred might display one AA sequence, from the reference, and your name column would have a different value from real experimental data). On the other hand, this option can be turned on and off, so a note on the track description page would help explain the difference. One can think of bigGenePred as a bed12 + 8 where a lot of the additional columns are really to help annotate a gene prediction track (name2, geneName, geneName2, geneType, and metadata about coding) that probably would not be useful for your track (another reason to probably not use it).