Getting "couldn't find matching transcriptome" with Gencode 40

thelovelab / tximeta

Transcript quantification import with automatic metadata detection

https://thelovelab.github.io/tximeta/

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Getting "couldn't find matching transcriptome" with Gencode 40 #64

Closed jwtobias closed 2 years ago

jwtobias commented 2 years ago

Counted with Salmon v 1.8.0 against human Gencode 40 (released 4/11/22) and getting the error below. When do you typically capture the gencode releases?

packageVersion("tximeta") [1] '1.12.4'

se <- tximeta(coldata) importing quantifications reading in files with read_tsv 1 2 3 4 5 6 couldn't find matching transcriptome, returning non-ranged SummarizedExperiment

mikelove commented 2 years ago

Oh I just missed this one. Let me push this one through now. Thanks for the note.

mikelove commented 2 years ago

I just pushed to GH, could you try devtools::install_github("mikelove/tximeta") and see if this works (you may need to restart R)?

jwtobias commented 2 years ago

All good now. Thanks for the quick response and the great tool!