bigPsl track in the assembly hub cannot be displayed in UCSC genome browser

[Liu, Yating]

Hello,

I generated an assembly hub of Drosophila biarmipes. The homology track (bigPsl format) cannot be displayed in the browser. I attached myHub to the email. The hub is public accessible through http://old-gep.wustl.edu/~galaxy/myHub/hub.txt

In trackDb.txt, the track type of pslToBigPsl_on_data_20.bb is bigPsl. If you upload this assembly hub url to the UCSC genome browser, it will show a blank page (see attachment blank_page). However, if you change the track type to bigBed 12 +, it can be showed in the browser. 

Please let me know if you have any questions. Thank you!

Best,

Yating

[Jairo Navarro Gonzalez]

Dear Yating,

Thank you for using the UCSC Genome Browser and reporting your issues with your assembly hub.
This is a known issue where bigPsl entries cause a crash if there is no sequence on the negative strand.
This issue is fixed and will be released in the next release cycle on February 7th, 2017.

One of our engineers suggested using bigBed since using bigPsl doesn't have many advantages if you aren't including the sequence. 

Using bigPsl instead of bigBed means that you get neither the alignment on the hgc page or mismatches in red on the Genome Browser display page.

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

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