Re: [Gmod-ajax] Requirements for a GFF3 to render properly?

[Scott C. <sc...@sc...>]

Another thing I should have mentioned when I said this looked like GTF: GTF
is frequently called GFF2.5. What you posted would also pass as GFF 2.

On Thu, Jan 11, 2024 at 2:45 PM Scott Cain <sc...@sc...> wrote:

> Hi Hans,
>
> I'd say the problem is primarily that the snippet you've shown isn't GFF3;
> it looks much more like GTF (GFF3 would have "tag=value;tag2=value2" in the
> ninth column, as opposed to 'tag "value"; tag2 "value2"' in the ninth
> column). While JBrowse 2 does support GTF, it has some drawbacks, the
> biggest of which is there isn't an indexed form of it, so the tracks will
> load very slowly since JBrowse has to load the entire file and parse it in
> order to draw any portion of it. If you had GFF3, each of the exon features
> would have a "Parent" tag that pointed to the ID of the parent transcript.
>
> The other thing that jumps out at me for the data snippet you provided is
> that all of the transcripts appear to share the same start and end
> coordinates of the child exons, so they would only show up as individual
> exons anyway. I would guess that elsewhere in your GTF file you have more
> complicated examples with transcripts that have multiple exon children.
>
> So, it's hard to say what I would expect to see without a better example
> of your GTF, but you probably want to look at generated GFF3 anyway, so
> that you can take advantage of tabix indexing of the GFF3 files.
>
> Of course, feel free to follow up with more questions or example data and
> we can figure out where to go from there.
>
> Scott
>
>
> On Thu, Jan 11, 2024 at 2:29 PM Hans Vasquez-Gross <hva...@un...>
> wrote:
>
>> Hello All,
>>
>> I have the output from isoseq collapse then pigeon index to create a
>> sorted .gff3 file for a new assembly. Currently, this gff3 file has
>> transcript and exon definitions.  However, when I load this track data on
>> JBrowse2, it shows the transcripts as one large unit and the exons as a
>> separate unit. It doesn't seem to correct render the intron/exon
>> boundaries. The annotation track is on top in yellow and the isoseq_reads
>> bam file is below.
>>
>> Example data:
>> ##pacbio-collapse-version 1.0
>> ##date Thu Jan 11 00:10:30 2024 UTC
>> ctg_p_c_003493_0_75000_89999 PacBio transcript 11587 12122 . - . gene_id
>> "PB.32086"; transcript_id "PB.32086.1";
>> ctg_p_c_003493_0_75000_89999 PacBio exon 11587 12122 . - . gene_id
>> "PB.32086"; transcript_id "PB.32086.1";
>> ctg_p_c_033075_0 PacBio transcript 20564 22031 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.1";
>> ctg_p_c_033075_0 PacBio exon 20564 22031 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.1";
>> ctg_p_c_033075_0 PacBio transcript 20564 21887 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.2";
>> ctg_p_c_033075_0 PacBio exon 20564 21887 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.2";
>> ctg_p_c_033075_0 PacBio transcript 20564 21758 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.3";
>> ctg_p_c_033075_0 PacBio exon 20564 21758 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.3";
>>
>>
>> Any suggestions?
>>
>> Thank you,
>> -Hans
>>
>> --
>>
>>
>>
>> [image: signature_998258195]
>>
>> *Hans Vasquez-Gross, Ph.D*
>>
>> Bioinformatics Scientist,
>> Nevada Bioinformatics Center
>>
>> https://www.unr.edu/bioinformatics
>>
>> hva...@un...
>>
>> _______________________________________________
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>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
> GMOD Project Manager (http://gmod.org/)
> 216-392-3087
> WormBase Developer (http://wormbase.org/)
> Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
> VirusSeq Project Manager (https://virusseq-dataportal.ca/)
> Human Cancer Models Initiative Project Manager (
> https://hcmi-searchable-catalog.nci.nih.gov/)
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)