[BioC] gff files: how to tell if right-open interval convention used?

[Hervé Pagès]

Hi karl,

On 03/30/2011 01:58 PM, karlerhard at berkeley.edu wrote:
>
> Hi all,
>
> I'm a grad student at UC Berkeley, I'm new to the list, as well as to R
> programs in general, so I hope you'll forgive my simplistic questions.
>
> I'm working with the girafe package to generate counts table which can be
> input into edgeR.  I've noticed that the readGff3 function is sensitive to
> whether the gff file being read uses this "right-open interval convention"
> or not.  I'm just not sure how to tell if the gff file I am using follows
> this convention.  Is there a simple way to find out?

Valid GFF3 files should never use the "right-open interval convention".
Always 1-based starts and ends:

   http://www.sequenceontology.org/gff3.shtml

Look at the first line in your file. If you see:

##gff-version 3

then the file claims to be adhering to the GFF3 specs.

Of course, you can never be 100% sure. How much do you trust the tool
that generated your GFF3 file? Is it documented? Do you have access
to its source code?

Cheers,
H.


>
> Any help on this would be greatly appreciated.
>
> best,
>
> karl
>
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-- 
Hervé Pagès

Program in Computational Biology
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