Re: [Gmod-ajax] JBrowse2 loading human hg38

[Vaneet L. <van...@uc...>]

The fasta and a gtf file was sourced from here:

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

I just learned my colleague had to convert the gtf to gff3 format, maybe there’s something that went wrong during the conversion?

What does that error usually indicate though?  I assumed it was gene models that referenced a parent ID that doesn’t exist in the file anywhere, but I couldn’t find any examples of that.

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: Wednesday, April 17, 2024 10:43 AM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse2 loading human hg38

[△EXTERNAL]

what is the source of "hg38.ncbiRefSeq.gff3.gz"?

-Colin

On Wed, Apr 17, 2024 at 12:36 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

Not sure if this is a JBrowse issue or one with the human genome or gene models, but this being human, it’s a fairly common genome so I though I’d ask the community in case they have ran into any issues when loading hg38 and its gene models.

So, I loaded the human hg38 version genome assembly (hg38.masked.fa.gz) and that worked fine.  I loaded the NCBI RefSeq gene models track (hg38.ncbiRefSeq.gff3.gz) for hg38 next and that seemed to load fine.  However, when I go to any of the standard chromosomes which have a short sequence ID (chr1, chr2, ..etc.) as opposed to the appended longer sequence IDs (chr8_KI270815v1_alt, chr9_GL383540v1_alt) I get this error (stack trace):


Error: some features reference other features that do not exist in the file (or in the same '###' scope). PRAMEF30P,RNU6-1072P,PRAMEF29P,PRAMEF28P,PRAMEF35P,PRAMEF31P,PRAMEF32P,RNU6-771P,MT1XP1,RPL22P3,RNU1-6P,TRV-CAC11-1,PDE4DIPP8,LOC101056699,EIF1AXP1,TRV-CAC13-1,CROCCP4,PDE4DIPP9,TRV-CAC11-2,LOC124903860,RNU1-5P,LOC107985101,RPL29P6,DPPA2P2,RN7SL679P,RPL36AP9,RPL31P12,LOC100131348,SLC25A24P1,NBPF5P,SLC25A24P2,ST13P21,LOC100420170,LOC124904641,LOC107985110,GEMIN2P1,RN7SL372P,LOC645965,MTX1P1,MPTX1,OR10J2P,OR10J7P,OR10J8P,OR10J9P,LOC100996886,PEBP1P3,ST13P19,RNASEH1P3,RNU5A-8P,BPNT2P1,RPL23AP15,H2BU2P,RNA5SP19,RNA5SP18,LOC124900442,FTH1P2,LOC100418822,RPS21P1,MTCYBP14,MTND6P14,MTND5P19,MTND4P10,MTND4LP21,MTND3P8,MTCO3P46,SEPTIN14P21,CICP21,RNU6-747P,FCF1P7,FABP7P1,VN1R17P,OR2AS2P,OR2AS1P
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finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856<mailto:finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856>
parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409<mailto:parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409>
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JBrowse 2.10.3

This error was on chr1 but as I said it happens for pretty much any standard chromosome I go to.  When I go to the ‘alt’ or ‘random’ sequences with the longer sequence names, they seem to load gene models fine.  When I check those mentioned gene models in the error, I can’t seem to find anything wrong with its references.

Just wanted to check in case someone has ran into the same error and how it was resolved.

Thanks,

Vaneet
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