Problem with the Table browser

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Anushree Sanyal

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Aug 16, 2016, 11:37:57 AM8/16/16
to gen...@soe.ucsc.edu
Dear All,

I am building an Assembly Hub. I can visualize the alignment when I paste the URL (https://export.uppmax.uu.se/b2011231/cactus/progressiveAlignment/hub.txt) in the My Hubs field. I have attached a screen shot. I can visualize the alignment. However, the table browser is not working and I get this error message:
"Couldn't connect to database hub_102373_Anc0 on mysqlrr as hguser.
Unknown database 'hub_102373_Anc0'. I also cannot get the custom track to work when I try to generate my own custom track from my own data. I have also been trying to upload a GFF file of Neurospora crassa which is the reference genome, but I am getting errors. I have checked that the file is tab-delimited and also that the chromosomes are specified as chr1 and not Chr1 or 1. It still doesn't seem to work.

I have aligned five genomes of which one is the reference genome. What do I need to do to make the table browser work? I would like to look at structural variation in several strains of Neurospora.
 
Thanks so much for your time and help in advance.

Best regards,
Anushree
Anc0 Anc0refChr907:1-1000 - UCSC Genome Browser v336.html

Cath Tyner

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Aug 16, 2016, 1:46:35 PM8/16/16
to Anushree Sanyal, gen...@soe.ucsc.edu
Hello Anushree,

Thank you for reporting the issues you are having with the Table Browser and custom tracks for your hub.

First - the Table Browser error:

To confirm, are you using the public web site at http://genome.ucsc.edu and not a mirror or the GBiB virtual browser? Are you still experiencing this issue?

I could not replicate your Table Browser error. I was able to successfully load your hub, where I then went to the Table Browser. From the Table Browser, I was able to export MAF output for all six of your genomes.

As an alternative to a screen shot or html file of your web page, you can send a link to a "saved session." For example, here is a link to my "saved session" where I loaded your hub. You should be able to click on th
​is​
​ session​
link
 and get MAF output for your genome assemblies.

You can read more about creating sessions on the Sessions User Guide
​. Sessions can​
 be created from the site-wide menu "My Data > My Sessions."

If you get a chance, it might be helpful for you to send us a saved session where you are getting the Table Browser error.

Second - the custom track issue:

For your custom track, you will need to use whatever chrom names you have used in your assembly hub. For Anc0, it appears that you are using the naming convention "Anc0refChr*", so you will need to change your custom track to reflect those names.

Please respond to this list if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser. 
​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E
mail 
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​ or search the Public Archives
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​Enjoy,​
Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support
UC Santa Cruz Genomics Institute


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Anushree Sanyal

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Sep 14, 2016, 2:24:36 PM9/14/16
to Cath Tyner, gen...@soe.ucsc.edu
Hi Cath,

As you mentioned in the earlier email, I was able to export the MAF format of the files through the Table Browser. However, I can export only one genome at a time which is aligned to the reconstructed ancestrat genome which is Anc0 in my case. How can I export a file which contains an alignment which includes the alignment of all the five genomes to Anc0 in this case? It would be easier if I had all the five genome tracks in a single alignment exported as a single MAF file so that I can directly compare them instead of going through five separate pairwise alignments against Anc0. How do I go about this issue?

Thanks you fr your time and help.
Kind regards,
Anushree

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Matthew Speir

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Sep 15, 2016, 12:18:35 PM9/15/16
to Anushree Sanyal, Cath Tyner, gen...@soe.ucsc.edu
Hi Anushree,

Thank you for your question about obtaining your HAL alignments in MAF format.

Unfortunately, there is not a way to do this using the Table Browser. However, you may be able to use the "hal2maf" utility provided with the other progressiveCactus tools to do this. For example, you can use the following example to convert a portion of your HAL file into MAF format:

hal2maf --refSequence Anc0refChr907 --length 1000 https://export.uppmax.uu.se/b2011231/cactus/progressiveAlignment/neurospora.hal my.maf

While in this case, I've specified a remote HAL file, you can replace that with a path to the file on your local machine. Additionally, you can replace the output file "my.maf" with whatever name you would like.

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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