Do you offer any benchmarks of quality and quantity of known and predicted genes shown in the assembly tracks from RefGene, Acembly, Ensembl, Genscan, Fgenesh++, and TIGR Gene Index?”
Response: These tracks are contributed by institutional programs outside of UCSC. You can access links to their home pages and relevant publications from the description pages associated with the tracks (which can be viewed by clicking on the grey mini-button to the left of the track). You can also obtain information from the Users Guide and the Credits page. Methods and quality checks are often described in greater detail there. No uniform benchmarking system exists. Finished chromosomes 20-22 are commonly used, but even here the experimental work continues today on delineating genes. Currently no summary statistics are offered by UCSC; however, these are easily compiled from the appropriate tables in the table browser. The number of predicted genes and exons are easily compared. Some quality checks can also easily be run, such as how many of the predicted gene models are incomplete (eg, transcription start coordinate same as CDS start?). Looking at almost any genome browser window, y
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