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

[Hans Vasquez-G. <hva...@un...>]

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


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[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>