JBrowse (and Tablet) only show Ensembl transcripts/can't search by gene ID or symbol
Entering edit mode
4.0 years ago
mamillerpa ▴ 40

I have deployed a JBrowse site, following http://jbrowse.org/code/JBrowse-1.14.1/docs/tutorial/

It's based on Ensembl 74 mouse. I'm pretty happy with how it's coming along, but I can't seem to see the Ensembl genes, or search with gene IDs or gene symbols. I do see, and can search on transcript IDs.

The gene ID and symbol values are present in the GFF3 file... but maybe not in the right pace? Maybe I need to import the GFF3 into JBrowse with come custom field specification?

mark@office:/var/www/html/jbrowse$ head Mus_musculus.GRCm38.74.gff3
# gffread-0.9.12.Linux_x86_64/gffread -E Mus_musculus.GRCm38.74.gtf -o-
# gffread v0.9.12
##gff-version 3
1       unprocessed_pseudogene  transcript      3054233 3054733 .       +       .       ID=ENSMUST00000160944;geneID=ENSMUSG00000090025;gene_name=Gm16088
1       unprocessed_pseudogene  exon    3054233 3054733 .       +       .       Parent=ENSMUST00000160944
1       snRNA   transcript      3102016 3102125 .       +       .       ID=ENSMUST00000082908;geneID=ENSMUSG00000064842;gene_name=Gm26206
1       snRNA   exon    3102016 3102125 .       +       .       Parent=ENSMUST00000082908
1       processed_transcript    transcript      3205901 3216344 .       -       .       ID=ENSMUST00000162897;geneID=ENSMUSG00000051951;gene_name=Xkr4
1       processed_transcript    exon    3205901 3207317 .       -       .       Parent=ENSMUST00000162897
1       processed_transcript    exon    3213609 3216344 .       -       .       Parent=ENSMUST00000162897

I'm seeing the same kind of thing in Tablet. Gene IDs and names/symbols are included as tags on transcripts

GFF type: TRANSCRIPT Name: ENSMUST00000082388 Padded: 70 to 1,024 Unpadded: 70 to 1,024 Tags: ID=ENSMUST00000082388 geneID=ENSMUSG00000064337 gene_name=mt-Rnr1

Here's how I prepared my JBrowse:

bin/prepare-refseqs.pl Mus_musculus.GRCm38.74.dna.primary_assembly.fa

gffread -E Mus_musculus.GRCm38.74.gtf -o- > Mus_musculus.GRCm38.74.gff3

bin/flatfile-to-json.pl --gff Mus_musculus.GRCm38.74.gff3 --trackType CanvasFeatures \
    --trackLabel Mm74gff

bin/add-bam-track.pl --label 3_1_reads --bam_url my_sorted_indexed.bam --in data/trackList.json

bin/generate-names.pl -v

enter image description here

jbrowse ensembl tablet • 1.5k views
Entering edit mode
4.0 years ago
mamillerpa ▴ 40

In JBrowse, I had to specify the attributes that I wanted when importing the GFF3 annotations

bin/flatfile-to-json.pl -gff Mus_musculus.GRCm38.74.gff3 \
    --trackType CanvasFeatures --trackLabel MmEns74_features  \
    --nameAttributes "name,id,ID,geneID,gene_name"

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