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tseemann / barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor
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Fasta file and GFF have shifted start of 16S #37

Closed sleyn closed 4 years ago

sleyn commented 4 years ago

Hello!

I'm using barrnap 0.9 Interesting observation that GFF file start positions are shifted by +1 compared to FASTA header start:

NC_009053 barrnap:0.9 rRNA 69357 70894 0 + . Name=16S_rRNA;product=16S ribosomal RNA

>16S_rRNA::NC_009053:69356-70894(+)

Is this a bug or feature?

tseemann commented 4 years ago

@sleyn the problem occurs because BED files and GFF files use different coordinate systems. The FASTA file is generated by bedtools so it uses 0-based/end-exclusive while GFF uses 1-based/end-inclusive.

So yes it's kind of a bug in that the GFF and FASTA (via BED) are inconistent.

sleyn commented 4 years ago

Ok, thanks for explanation!