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

[karlerhard at berkeley.edu]

Thanks for the answers, very helpful.  I was a bit confused reading the
help page for the readGff3 function, which states:

"When the GFF file follows the right-open interval convention (isRightOpen
is TRUE), then GFF entries for which end base equals first base are
recognized as zero-length features and loaded as inter_base intervals."

This suggests that there are gff files out there that have this right-open
interval convention.  I will just have to find out the source of the
particular gff file I'm using (which describes a filtered gene list for
maize) to determine whether it uses this convention or not.  Though based
on your comments, I think I should assume that it is 1-based closed.



> karl,
>
> GFF should always be 1-based closed, not 0-based right-open (unlike BED
> format).  I think this convention goes back to the original version of GFF
> from Sanger up to the latest version, GFF3.
>
> So, it probably comes down to whether the source of the GFF output you are
> using is generating the correct coordinates, not how R/BioC is processing
> it.  Unless the girafe method in question is allowing BED output to be
> read as well (I would consider that bad).
>
> chris
>
> On Mar 30, 2011, at 3:58 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?
>>
>> Any help on this would be greatly appreciated.
>>
>> best,
>>
>> karl
>>
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>
>