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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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tximeta UCSC not co-operating in terms of mm10 #58

Closed justinjacobse closed 2 years ago

justinjacobse commented 2 years ago

(Edit: title of issue is supposed to be "tximeta and UCSC not co-operating in terms of mm10")

Hello, when I try to run tximeta, I get this error:

fetching genome info for GENCODE Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE

I found that others have had a similar problem when using GenomeInfoDb due to UCSC releasing a patch update for mm10 (see https://github.com/Bioconductor/GenomeInfoDb/issues/27 and https://www.biostars.org/p/9477823/)

They provide a workaround, but I don't know how to integrate the workaround with tximeta.

I am using tximeta 1.8.2, and I know the most recent version is 1.11.2. Is this issue fixed in the new version? (If not, I would rather not update it because every time I update a package in R, another package stops working).

Thank you!

mikelove commented 2 years ago

You can either use skipSeqinfo=TRUE, which avoids using USCS to grab seq info, or you can get the latest version of GenomeInfoDb which resolves the issue (the issue you linked to is now closed by Herve).

justinjacobse commented 2 years ago

Thank you so much! skipSeqinfo=TRUE worked perfectly.