Hi all,
If you've been having similar trouble, or if you were following this
thread for the solution.
The "exon linking" in artemis only works with GFF under one condition:
There must be a gene, an mRNA for (more than one) exons to be linked.
The exons should have the mRNA feature (ID) as a Parent and the mRNA
feature must have the gene feature (ID) as a Parent. The linking will
not work if the GFF files only has mRNA and exons (exons having mRNA
as parent) nor if it only has gene and exons (exons having gene as
parent) nor if it only has gene and mRNAs (mRNAs having gene as
parent).
So, in order to link the exons, I gave each mRNA a gene feature having
same coordinates as the mRNA feature. Then I made the gene parent to
mRNA and the mRNA parent to the multiple exons. In this case, it's
great that the mRNA feature is hidden, else, it'll look too messy with
both gene and mRNA feature being visible.
All the best and cheers,
-- yealing --
On Tue, Sep 20, 2011 at 7:13 PM, Tim Carver wrote:
> Hi Yealing
>
> This should work and I am not sure why your not seeing that. For example:
>
> chr1 artemis gene 210 720 . + . ID=x
> chr1 artemis mRNA 210 720 . + .
> ID=x.rna;Parent=x
> chr1 artemis exon 210 280 . + . Parent=x.rna
> chr1 artemis exon 291 720 . + . Parent=x.rna
>
> this uses the Parent qualifier of the mRNA to join the two exons.
>
> The mRNA's are greyed out but you can still select and edit them. There
> should be an option to change this (and there is with chado database
> entries) so I will include that for GFF entries. When you right click on the
> feature display there will then be an option to 'Show/Hide Features...'.
> This will appear in the next development release.
>
> Regards
> Tim
>
> On 9/20/11 9:06 AM, "Yealing" wrote:
>
>> Hi All
>>
>> I've switched over to using GFF3 some time ago simply because it's the
>> preferred file format for most software. Since then, I've been having
>> some problem in artemis. I've tried to dig, but maybe because I have
>> not digged deep enough... Please, anyone, if you can help.
>>
>> During annotation, I write GFF3 files according to the guide on
>> http://www.sequenceontology.org/gff3.shtml. However, because there
>> isn't an artemis GFF validator, valid GFF3 files still have problems
>> in artemis. The Parent tag is supposed to be able to group exons into
>> transcripts (mRNA?) and transcripts into genes. However, the features
>> with identical Parent tags are not linked in artemis. Why is this so?
>>
>> I also have problems with features I mark as mRNAs. When I load the
>> GFF files in artemis, in most cases the mRNA are greyed out in the
>> feature list. I rana search and found in one of the artemis paper that
>> this means the feature is "hidden". But I could not find a switch to
>> "unhide" it. When I generate new mRNA feature in artemis, it is not
>> hidden by default. Can I change this? If not, can I at least unhide it
>> individually?
>>
>> Thank you!
>> Yealing.
>>
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>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
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