mRNA and protein sequence for custom assembly hub

[Eyal Ben David]

Hi,

I've preparing a custom assembly hub for an organism we've sequenced and predicted genes for. I was able to get a genepred track to display correctly our ab initio gene prediction. I'd like to be able to extract predicted mRNA and protein sequences in the assembly hub (as is possible for the assemblies on the website). I wanted to ask how to achieve that.

Thanks,

Eyal


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Eyal Ben-David, PhD

Post-doctoral Scholar

Lab of Prof. Leonid Kruglyak

Department of Human Genetics

David Geffen School of Medicine

UCLA

[Matthew Speir]

Hi Eyal,

Thank you for your question about bigGenePred tracks in hubs.

Could you provide more information about what you are looking for on your bigGenePred tracks? From what I can tell the "Translated Protein from genomic DNA", "Predicted mRNA", and "Genomic Sequence from assembly" links show up on the details page for items in both bigGenePred custom and hub tracks.

Here you can see these links appearing on an example bigGenePred hub: http://genome.ucsc.edu/cgi-bin/hgc?db=hg38&c=chr1&l=11102836&r=11267747&o=11106534&t=11262507&g=hub_180419_bigGenePred2&i=ENST00000361445.5

Additionally, could provide a link to your hub so that we can attempt to debug any issues on our end? You can share the link to your hub with me privately if you do not wish to share it with the public list.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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