zero-based stop positions in BED files for splice junctions

[bzip2]

Hi.

Please check my math, but it looks like the stop positions in recount BED files for splice junctions are 0-based instead of 1-based.

Here is an example. I choose a small study at random and click on jx_bed. Here are two KnownGene junctions from this file:

chr1 1407019 1407129 ... -
chr1 1486235 1486542 ... +

In real-life (UCSC browser 1-based coordinates), the first intron goes from 1407020 to 1407130, and the second from 1486236 to 1486543. Stop positions are 1-based in BED format. I hate that too. :O)

It would be useful to include a comment in the files themselves or in the file info column to the effect that these are zero-based intronic hg38 coordinates, and assuming you don't want to re-create all the files, to call the files something other than BED.

Thanks.

[lcolladotor]

Hi,

Thanks for creating an issue.

This has been listed under the known issues in the main website since we noticed it at https://jhubiostatistics.shinyapps.io/recount/ (see https://github.com/leekgroup/recount-website/blob/master/website/ui.R#L123-L124).

We don't really plan on remaking the BED files. The issue was fixed in Rail-RNA a while back. So I suspect that we won't update the BED files until the samples are re-processed (if/whenever we update recount2). @nellore might have more to say.

I'll leave the issue open as a low priority one.

[lcolladotor]

This will be fixed in recount3, though that will involve completely new files so the ones in recount2 won't be updated/fixed.

Best,
Leo