Hello Biostars comunity,
For my project, I'm working with the transcriptome of a non-model organism, which has an incomplete and in many cases incorrect reference annotation. As such, I have to manually inspect the gene models, and compare them with assembled transcripts, long reads alignment, etc. I've using Jbrowser for the last 2 months, however, this software crashes every time I try to change scaffold or even if I load 4 or 5 tracks. This makes my job much less productive.
Does anyone have experience with this kind of problem, and as found a workaround, solution? (i.e using another more optimized genome browser?).
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Rogerio Ribeiro •
For genome annotation tool I'm currently working with MIKADO to refine my transcriptome assembly. However, I want to be able to inspect some results and visualize my candidate genes. I'll check Artemis for visualization.
In a follow up email to the OP we found that what was needed was to load tabix indexed GFF instead of plain GFF
The unindexed GFF caused slowness on scaffold switches
To create indexed GFF my general strategy is
sudo apt install genometools
gt gff3 -sortlines -tidy -retainids source.gff > source.sorted.gff
bgzip source.sorted.gff
tabix source.sorted.gff.gz
Then loading source.sorted.gff.gz and the tabix index for it into jbrowse helps
GenomeView might be an other option worth investigating . It does both browsing, visualization as well as a gene editing tool
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Hi there, I'm a jbrowse dev. If you are interested feel free to send me an email colin.diesh@gmail.com I can check out what you're looking at...definitely would be interested to help :)