GFF output and Fasta-headers give different start-coordinates of rRNA-genes

[jvollme]

Barrnap v.0.9 produces gff-output and (optionally) a fasta output. The fasta output has the coordinates of each rRNA prediciton in the header, but not the evalue of that prediction. The gff output has also the evalue.

I now noticed that the start positions given in the fasta headers differ from the start positions given in the gff-output (usually by a value of 1).
For me this is a bit of a problem, because in order to catch any possible variation of rRNA genes in metagenomic bins, I am running barrnap runs for all three kingdoms (bac, arc & euk) consecutively and then try to identify overlapping hits and keep only the highest scoring (i.e. lowest evalue) hit for each overlapping possibility.
This means I have to compare the gff output (in order to get the evalues) with the fasta-headers.

Is this difference perhaps a bug or is it due to some special gff-specifications?
Can i safely assume that it is off by exactly 1 in ALL cases in order to correct for this difference, or could it be a bit more problematic?

Alternatively, it would be most helpful to either add the corresponding fasta seqid to the gff-output, or the evalue to the fasta-header.

[tseemann]

@jvollme you are right
i realise now that the FASTA comes from bedtools which uses [0,L) coordinates while GFF uses [1,L] coordinates.