What’s the Answer? (zero-based, one based coordinates)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted item at Biostars is not so much a question, but an answer. It’s a very nice explanation of the off-by-one problem that so frequently bites bioinformaticians in the bits. Here are some examples from earlier this year:

I won’t recopy the post over here, because you should see it in full over at Biostars with the very helpful illustrations. You should bookmark this and save yourself whiteboard time in the future. As you can see over there, it got very high scores for helpfulness.

Tutorial: Cheat sheet for one-based vs zero-based coordinate systems

I am frequently faced with variant files of either 0-based or 1-based coordinates and having to determine which I am looking at and how to convert between them. I usually go to the white board and work it out. This time, I figured I would just create a digital copy….

[go see the details and helpful illustrations over there]

Obi Griffith

You’ll need this. Trust me. So many times I’ve had to address this in UCSC Genome Browser trainings, usually with SNP locations.