This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Are gencode gtfs really one-indexed for the start- and zero-indexed for the end-coordinate?

I am looking at the schema for gencode gtfs and it claims the starts are one-indexed, but does not mention what indexing the ends use. I do not want to blithely assume that the ends are also 1-indexed, because the UCSC database dumps use 0-indexing for the start and one-indexing for the end so it might be that gencode uses the reverse format.

Does anyone know for sure? Sources or how you came to know/computed the answer would be nice.

gencode gtf
• 5,834 views • link
updated by Ram Ram • written by Endre Bakken Stovner Endre Bakken Stovner

1 answer

Both are one-indexed: http://www.ensembl.org/info/website/upload/gff.html

  1. start - Start position of the feature, with sequence numbering starting at 1.
  2. end - End position of the feature, with sequence numbering starting at 1
• 0 views • link
updated by Ram Ram • written by Endre Bakken Stovner Endre Bakken Stovner

I would just note it is not just the indexing but whether the interval is open ended or closed (inclusive) at the coordinates. These concepts do not mean the same thing - even though the UCSC may describe it that way, I think that just makes things more confusing. The UCSC coordinates are zero based, and open ended at the upper limit.

You are correct that the GTF is both indexed from 1 and also includes both coordinates that are listed.

• 0 views • link
updated by Ram Ram • written by Istvan Albert Istvan Albert

Log in to answer this question.

More posts like this