Track hub and assembly hub
Sarah Djebali
Matthew Speir
Thank you for your question about assembly hubs in the UCSC Genome Browser.
When I connect your hub, it appears to load fine and I'm able to view your hub through the genome gateway page: http://genome.ucsc.edu/cgi-bin/hgGateway. Assemblies from hubs can be found at the top of the list of genomes on the left-hand side of the page.
However, when I attempt to view this genome, I see the error:
Couldn't open http://genoweb.toulouse.inra.fr/~sdjebali/fragencode/mixhub/2018/groups.txt
at the top of the page. This error indicates that you reference this "groups.txt" file in your genomes.txt file, but the file is not actually present in the directory: http://genoweb.toulouse.inra.fr/~sdjebali/fragencode/mixhub/2018/. You either need to create this file, or remove the reference to it in your genomes.txt file. Since it looks like you don't use custom groups in your trackDb.txt file, you could probably just remove the offending line from your genomes.txt.
One other comment on your hub, for your genome, you should create a new htmlPath path page. The current one, which looks to just be a copy of an NCBI page, doesn't interact well with Javascript and HTML already present on the page. You can see this here: http://genome.ucsc.edu/cgi-bin/hgGateway?genome=capHic102&hubUrl=http://genoweb.toulouse.inra.fr/~sdjebali/fragencode/mixhub/2018/hub.txt. A good example of an assemblyl description page can be found in the C_elegans_isolates assembly hub here: http://waterston.gs.washington.edu/trackhubs/isolates/CB4856Princeton_Contigs/description.html.
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
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAMLQFOU7mouyg8ybbJ1Bdo1DsUNVNf7tK%3DzokhG8D%3Dg12wWy%3DA%40mail.gmail.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.
Sarah Djebali
Hi Sarah,
Thank you for your question about assembly hubs in the UCSC Genome Browser.
When I connect your hub, it appears to load fine and I'm able to view your hub through the genome gateway page: http://genome.ucsc.edu/cgi-bin/hgGateway. Assemblies from hubs can be found at the top of the list of genomes on the left-hand side of the page.
However, when I attempt to view this genome, I see the error:
Couldn't open http://genoweb.toulouse.inra.fr/~sdjebali/fragencode/mixhub/2018/groups.txt
at the top of the page. This error indicates that you reference this "groups.txt" file in your genomes.txt file, but the file is not actually present in the directory: http://genoweb.toulouse.inra.fr/~sdjebali/fragencode/mixhub/2018/. You either need to create this file, or remove the reference to it in your genomes.txt file. Since it looks like you don't use custom groups in your trackDb.txt file, you could probably just remove the offending line from your genomes.txt.
One other comment on your hub, for your genome, you should create a new htmlPath path page. The current one, which looks to just be a copy of an NCBI page, doesn't interact well with Javascript and HTML already present on the page. You can see this here: http://genome.ucsc.edu/cgi-bin/hgGateway?genome=capHic102&hubUrl=http://genoweb.toulouse.inra.fr/~sdjebali/fragencode/mixhub/2018/hub.txt. A good example of an assemblyl description page can be found in the C_elegans_isolates assembly hub here: http://waterston.gs.washington.edu/trackhubs/isolates/CB4856Princeton_Contigs/description.html.
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
On 12/7/17 11:38 PM, Sarah Djebali wrote:
--
---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAMLQFOU7mouyg8ybbJ1Bdo1DsUNVNf7tK%3DzokhG8D%3Dg12wWy%3DA%40mail.gmail.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.
Jairo Navarro Gonzalez
Hello Sarah,
Thank you for using the UCSC Genome Browser and your follow-up question.
I am no longer seeing the error and am able to load your assembly hub into the genome browser. You can access your goat assembly by going to the top of the list of genomes on the left-hand side of the gateway page. Once at the top of the list, you will see your assembly hub:
FR-AgENCODE 2018
Selecting this hub, you will be able to display your goat assembly by clicking Go on the gateway page. Unfortunately, searching for capHic102 will not find your user uploaded goat assembly.
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.
Jairo Navarro
UCSC Genomics Institute
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAMLQFOXVUmR0m2-mr663px%3De3_-Yzb-jhVixvM42y2%3D8TyBxCw%40mail.gmail.com.
Sarah Djebali
Hello Sarah,
Thank you for using the UCSC Genome Browser and your follow-up question.
I am no longer seeing the error and am able to load your assembly hub into the genome browser. You can access your goat assembly by going to the top of the list of genomes on the left-hand side of the gateway page. Once at the top of the list, you will see your assembly hub:
FR-AgENCODE 2018
Selecting this hub, you will be able to display your goat assembly by clicking Go on the gateway page. Unfortunately, searching for capHic102 will not find your user uploaded goat assembly.
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.
Jairo Navarro
UCSC Genomics Institute
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
On Mon, Dec 11, 2017 at 2:34 AM, Sarah Djebali <sarah.djeb...@inra.fr> wrote:
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAMLQFOXVUmR0m2-mr663px%3De3_-Yzb-jhVixvM42y2%3D8TyBxCw%40mail.gmail.com.