Re: [Gmod-ajax] Question about GFF track rendering

[Colin <col...@gm...>]

Here are a couple tips that may help

https://jbrowse.org/docs/faq.html#my-canvasfeatures-don-t-show-up-with-subfeatures-why-not

The first rule, that you must set transcriptType, was relaxed in recent
versions so adding subParts: "exon" should be sufficient

-Colin

On Thu, Apr 29, 2021 at 5:43 PM Hans Vasquez-Gross via Gmod-ajax <
gmo...@li...> wrote:

> Hi JBrowse Team,
>
> I have two GFFs, both which have been converted from GTF using gff read
> then gt gff3 to sort.  However, one of my GFF files is not displaying exons
> on the browser. It is only displaying the transcript line but not the exon
> boundaries.
>
> [image: Screenshot from 2021-04-29 14-35-34.png]
>
> The second track I used stringtie to generate a merged GTF track from an
> RNAseq project. However, it doesn't seem to define CDS, only transcript and
> exons. Could this be the source of the problem?
>
> Below I'll give an excerpt of each GFF file:
> *1st working GFF*
> # gffread -E Astyanax_mexicanus.Astyanax_mexicanus-2.0.103.gtf -o-
> # gffread v0.11.7
> 1       ensembl exon    19172   19231   .       -       .
> Parent=ENSAMXT00000042139
> 1       ensembl CDS     19172   19231   .       -       0
> Parent=ENSAMXT00000042139
> 1       ensembl transcript      19172   27555   .       -       .
> ID=ENSAMXT00000042139;geneID=ENSAMXG00000035673
> 1       ensembl exon    19778   20349   .       -       .
> Parent=ENSAMXT00000037267
> 1       ensembl transcript      19778   27555   .       -       .
> ID=ENSAMXT00000037267;geneID=ENSAMXG00000035673
> 1       ensembl CDS     20212   20349   .       -       0
> Parent=ENSAMXT00000037267
> 1       ensembl exon    20281   20349   .       -       .
> Parent=ENSAMXT00000042139
> 1       ensembl CDS     20281   20349   .       -       0
> Parent=ENSAMXT00000042139
> 1       ensembl CDS     21829   21981   .       -       0
> Parent=ENSAMXT00000042139
> 1       ensembl CDS     21829   21981   .       -       0
> Parent=ENSAMXT00000037267
> 1       ensembl exon    21829   21981   .       -       .
> Parent=ENSAMXT00000037267
> 1       ensembl exon    21829   21981   .       -       .
> Parent=ENSAMXT00000042139
> 1       ensembl CDS     22129   22218   .       -       0
> Parent=ENSAMXT00000042139
> 1       ensembl exon    22129   22218   .       -       .
> Parent=ENSAMXT00000042139
> 1       ensembl exon    22129   22218   .       -       .
> Parent=ENSAMXT00000037267
> 1       ensembl CDS     22129   22218   .       -       0
> Parent=ENSAMXT00000037267
> 1       ensembl CDS     23160   23234   .       -       0
> Parent=ENSAMXT00000042139
> 1       ensembl exon    23160   23234   .       -       .
> Parent=ENSAMXT00000042139
> 1       ensembl exon    23160   23234   .       -       .
> Parent=ENSAMXT00000037267
> 1       ensembl CDS     23160   23234   .       -       0
> Parent=ENSAMXT00000037267
> 1       ensembl CDS     24621   24803   .       -       0
> Parent=ENSAMXT00000037267
> 1       ensembl CDS     24621   24803   .       -       0
> Parent=ENSAMXT00000042139
> 1       ensembl exon    24621   24803   .       -       .
> Parent=ENSAMXT00000042139
> 1       ensembl exon    24621   24803   .       -       .
> Parent=ENSAMXT00000037267
> 1       ensembl CDS     27412   27555   .       -       0
> Parent=ENSAMXT00000037267
> 1       ensembl CDS     27412   27555   .       -       0
> Parent=ENSAMXT00000042139
> 1       ensembl exon    27412   27555   .       -       .
> Parent=ENSAMXT00000042139
> 1       ensembl exon    27412   27555   .       -       .
> Parent=ENSAMXT00000037267
>
>
> *2nd non-working GFF*
> # gffread -E merged.gtf -o-
> # gffread v0.11.7
> 1       StringTie       exon    19172   19231   1e+03   -       .
> Parent=ENSAMXT00000042139
> 1       StringTie       transcript      19172   27555   1e+03   -       .
>       ID=ENSAMXT00000042139;geneID=MSTRG.2
> 1       StringTie       exon    19778   20349   1e+03   -       .
> Parent=ENSAMXT00000037267
> 1       StringTie       transcript      19778   27555   1e+03   -       .
>       ID=ENSAMXT00000037267;geneID=MSTRG.2
> 1       StringTie       exon    20281   20349   1e+03   -       .
> Parent=ENSAMXT00000042139
> 1       StringTie       exon    21829   21981   1e+03   -       .
> Parent=ENSAMXT00000037267
> 1       StringTie       exon    21829   21981   1e+03   -       .
> Parent=ENSAMXT00000042139
> 1       StringTie       exon    22129   22218   1e+03   -       .
> Parent=ENSAMXT00000037267
> 1       StringTie       exon    22129   22218   1e+03   -       .
> Parent=ENSAMXT00000042139
> 1       StringTie       exon    23160   23234   1e+03   -       .
> Parent=ENSAMXT00000042139
> 1       StringTie       exon    23160   23234   1e+03   -       .
> Parent=ENSAMXT00000037267
> 1       StringTie       exon    24621   24803   1e+03   -       .
> Parent=ENSAMXT00000037267
> 1       StringTie       exon    24621   24803   1e+03   -       .
> Parent=ENSAMXT00000042139
> 1       StringTie       exon    27412   27555   1e+03   -       .
> Parent=ENSAMXT00000042139
> 1       StringTie       exon    27412   27555   1e+03   -       .
> Parent=ENSAMXT00000037267
> ###
>
> Do you have any suggestions on how to get the second GFF displaying
> properly with exon boundaries on the transcript line?
>
> Thank you,
> -Hans
>
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