How to display gene names from gff3.gz file in Jbrowse


I’m trying to visualize genes from a gff3.gz file using JBrowse, with gff3.gz and fasta.gz files downloaded from NCBI into Galaxy. The gff3.gz file is not recognized by JBrowse, so it is displayed as a bed file, and as a result the “Type” column (third column) is displayed instead of the gene names (which are in the Attributes column 9). If I try and convert the gff3.gz dataset to a gff3 datatype before displaying in Jbrowse, then no genes or labels appear. If I download the gff3.gz file to my laptop and decompress and reupload, then the gene names do appear. I’m wondering if you can help me figure out how to display the gene names without downloading and decompressing first.

Here are my steps:

  1. download genome and gff3 into Galaxy

  2. Display in Jbrowse by selecting “genome from history” and adding a track “GFF/GFF3/BED Features”

Here is the history showing the gff3.gz file downloaded from NCBI, which does not display gene names in JBrowas, and the one that was downloaded, decompressed and reuploaded from my laptop, which does show gene names in JBrowse:

Thank you for any suggestions!

OK, I figured it out! If you run the “Convert”->“Convert compressed file to uncompressed file” and use the uncompressed file in JBrowse, it is read as the correct datatype and gene names are displayed. I’m wondering why it’s not decompressed automatically, as the fasta is. In any case, this solution works for me.

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