Coordinates for bed files should be 0 based, while gff is 1 based

[blakesweeney]

UCSC and ENSEMBL both define bed files as being 0 based:

https://genome.ucsc.edu/FAQ/FAQformat.html#format1 http://www.ensembl.org/info/website/upload/bed.html

while gff files are 1 based:

https://genome.ucsc.edu/FAQ/FAQformat.html#format3 http://www.ensembl.org/info/website/upload/gff.html

currently we export both files (at least for pome) as 1 based.

[mt1022]

The coordinates for human lncRNAs in bed and gff are still the same (both are 1-based in most recent release of RNAcentral: V9).

In addition, some lncRNA annotations are present in the gff file, but their coordinates are not present in the bed files.

[blakesweeney]

@mt1022 Thanks for point this out. We will only have BED files this release as part of our new genome mapping pipeline. We will add GFF files afterwards, and in doing so should fix the coordinate issue.