Patching hg38 2bit
Sebastien Weyn
Hello,
We are using minimal GBIC and have a blat query that seems to be returning a hit on chr15_ML143371v1_fix. Since we do not have that chromosome in our database, the blat output fails completely with the error “chr15_ML143371v1_fix is not in /gbdb/hg38//hg38.2bit”.
Could you please let me know how to patch the 2bit? Running sudo bash browserSetup.sh minimal hg38 was not sufficient.
Thanks!
Sebastien
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Brian Lee
Thank you for using the UCSC Genome Browser and a GBiC and your question about hg38 patch sequences.
Please try replacing your hg38.2bit in /gbdb/hg38//hg38.2bit with this file: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/hg38.2bit
The /latest/ will have patch sequences including chr15_ML143371v1_fix, that the online blat server is also using that your GBiC connects to when doing a Blat or PCR search. There are other options too, such as setting up a localized blat server and pointing to it.
Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please send new questions to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum to help others find answers to similar questions. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu, which is a private internal list to our support team.
All the best,
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Sebastien Weyn
Thank you so much! I hadn’t seen the “latest” directory. This fixed the issue.
Sebastien
From:
Brian Lee <bria...@soe.ucsc.edu>
Date: Wednesday, February 16, 2022 at 9:46 AM
To: Sebastien Weyn <sw...@stoketherapeutics.com>
Cc: genome...@soe.ucsc.edu <genome...@soe.ucsc.edu>
Subject: Re: [genome-mirror] Patching hg38 2bit
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