GenomeInfoDb (in R) and UCSC just stopped co-operating in terms of mm10

Question

[sami.kilpinen]

Hello,

Don't know how many have noticed but any function in GenomeInfoDb library (as well as ensembldb library) in R haven't been able to interact with UCSC servers what comes to mm10. Typical functions like Seqinfo(genome="mm10") return error Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE

I confirmed this separately both in local machine and in cluster computing resource machines. This worked last Friday, but since Monday morning this no longer works. I guess someone at UCSC already knows this, but just in case no, does anybody know whom this might actually concern there?

[jared.0.pollard]

I have also been experiencing this issue! I don't have any workaround at the moment but commenting to confirm that this is affecting multiple users, I hope it gets solved soon.

[lozzi]

I'm also experiencing this problem !!!! I've tried many things to get around it but it has completely derailed my pipeline.

[jared.0.pollard]

To be specific, I am experiencing issues with both "EnsDb.Mmusculus.v79" and "org.Mm.eg.db packages/libraries in R right now. There seems to be an ongoing discussion about this issue on GitHub, in case it is helpful to anyone.

https://github.com/Bioconductor/GenomeInfoDb/issues/27

[Maximilian Haeussler]

The bioconductor author will probably add a fix for this. There is a temporary workaround, by providing the old chrom.sizes file to the GenomeDb call, here is part of the response from the UCSC support team:

One option for the Bioconductor GenomeInfoDb tool is to use an earlier version of a similar file, https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.chrom.sizes, that will not have the _fix sequences or this specific chrna_GL456050_alt sequence, but this would require GenomeInfoDb to make these changes (also the mm10.chrom.sizes file is slightly different from the chromInfo.txt.gz in that chromInfo.txt.gz is gzipped and has one additional column explaining the data was generated from, in this case the updated "/gbdb/mm10/mm10.2bit" file allowing for these new patch sequences to be interactively viewed on the mm10 browser.

[jared.0.pollard]

Hi, thank you very much for this response. Would you be willing to explain how to actually go about doing this? I am a relative novice with R. How can I modify GenomeInfoDb to tell it to use the older file version?

Answer 1

[Luis Nassar]

Hello,

We recently added patch sequences to the mm10 assembly (http://genome.ucsc.edu/goldenPath/newsarch.html#080421) which broke some functionality with GenomeInfoDb.

They have since updated the package to support this change (https://github.com/Bioconductor/GenomeInfoDb/commit/a92e3979526f18812b5e6448d36271ab69aac690). So version 1.29.3 and above of GenomeInfoDb will have mm10 functionality back.

(Big thanks to Herve and the bioconductor team for the quick update)

If you have any follow up questions on the Genome Browser or its tools, our public help desk can always be reached at [e-mail]. You may also send questions to [e-mail] if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.