Assembly hub conservation track format
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Julia Chariker
Oct 20, 2015, 2:33:14 PM10/20/15
to gen...@soe.ucsc.edu
Hi,
I created an assembly hub that contains several data tracks. The hub functions well. However, on adding a conservation track in psl format, I encountered the following message:
ERROR: Unsupported type 'psl' in hub
On the UCSC website, it appears that this is an accepted format for custom tracks. Is there a particular format I should convert this to for use in an assembly hub?
Thanks for your help!
Julia Chariker
Robert Kuhn
Oct 21, 2015, 2:56:08 AM10/21/15
to Julia Chariker, UCSC Genome Browser Mailing List, Robert Kuhn
Hello, Julia,
It's nice to hear that you've made an assembly hub and find the
functionality useful
There are two approaches you might take. You could load your psl track
as it is by making it a custom track on your hub, or you could integrate
it into the hub in a binary format. The integrated track, like all hub
tracks, must be in a binary format, so you could convert the PSL to the
relatively new format, bigPsl or to a bigBed.
1. Load psl as a Custom Track.
After connecting the assembly hub, you can paste the psl data into the
Custom Track load box just as you would load a track onto one of the
assemblies hosted at UCSC. Or you could put the psl file in a web-accessible
location and load the URL as a Custom Track.
While the track would not actually be part of the hub, you could share the
hub and the custom track with others by constructing a compound URL as
decribed in the UCSC Genome Browser wikipedia entry:
https://en.wikipedia.org/wiki/UCSC_Genome_Browser#To_Host_Remote_User_Information
2. Convert to a binary format.
We recently released the utility, pslToBigPsl, as part of the source tree.
Though it has not yet been thoroughly tested and is also not yet documented,
you could use it to make a binary to include as a resident track in your hub.
The utility is found in our downloads section:
http://hgdownload.soe.ucsc.edu/admin/exe/
After unpacking the tarball, you can run the program with no arguments to
see the usage statement.
You could also convert the psl to a bed, then to a bigBed using the
appropriate utilities, pslToBed and bedToBigBed.
You should know that we will be releasing a new format, bigMaf, for
comparative genomics suitable for track or assembly hubs, though I cannot
offer a delivery date for this.
I hope this helps point you in a productive direction. If not, or if you
need us to be more specific, do not hesitate to contact us via the mailing
list.
best wishes,
--b0b kuhn
ucsc genome bioinformatics group
It's nice to hear that you've made an assembly hub and find the
functionality useful
There are two approaches you might take. You could load your psl track
as it is by making it a custom track on your hub, or you could integrate
it into the hub in a binary format. The integrated track, like all hub
tracks, must be in a binary format, so you could convert the PSL to the
relatively new format, bigPsl or to a bigBed.
1. Load psl as a Custom Track.
After connecting the assembly hub, you can paste the psl data into the
Custom Track load box just as you would load a track onto one of the
assemblies hosted at UCSC. Or you could put the psl file in a web-accessible
location and load the URL as a Custom Track.
While the track would not actually be part of the hub, you could share the
hub and the custom track with others by constructing a compound URL as
decribed in the UCSC Genome Browser wikipedia entry:
https://en.wikipedia.org/wiki/UCSC_Genome_Browser#To_Host_Remote_User_Information
2. Convert to a binary format.
We recently released the utility, pslToBigPsl, as part of the source tree.
Though it has not yet been thoroughly tested and is also not yet documented,
you could use it to make a binary to include as a resident track in your hub.
The utility is found in our downloads section:
http://hgdownload.soe.ucsc.edu/admin/exe/
After unpacking the tarball, you can run the program with no arguments to
see the usage statement.
You could also convert the psl to a bed, then to a bigBed using the
appropriate utilities, pslToBed and bedToBigBed.
You should know that we will be releasing a new format, bigMaf, for
comparative genomics suitable for track or assembly hubs, though I cannot
offer a delivery date for this.
I hope this helps point you in a productive direction. If not, or if you
need us to be more specific, do not hesitate to contact us via the mailing
list.
best wishes,
--b0b kuhn
ucsc genome bioinformatics group
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