The UCSC Genome Browser Team is clear about that the genome browser GUI indexing which is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All UCSC tables are indexed at 0-based, half-open intervals.

However, I can't seem to find a list of how resources are indexed at Cellbase. I know genomic sequence queries are 1-based and closed-interval, but are all the other tables? I could come up with tests for each resource I use at Cellbase, but I'd need a known true value for each test, which is impossible or impractical for most resources I need.

It's such a fundamental thing to know that there's probably a description somewhere, but I can't seem to find it. Or maybe there is a method to easily know, but I don't know that method. I've looked at:

  • the Cellbase website,
  • the Cellbase wiki (down for maintenance as of 3/11/20), and
  • I've read both the original NAR paper and
  • the recent BMC Bioinformatics paper on the pycellbase library (which I'm super-excited to try).

There is no mention of how nucleotides are counted. I'm sure I'm missing something; any help would be appreciated.


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