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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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couldn't find matching transcriptome, returning non-ranged SummarizedExperiment #50

Closed Alexander-Suen closed 3 years ago

Alexander-Suen commented 3 years ago

Hi Mike, My tximeta version is 1.8.1 but I still met the error "couldn't find matching transcriptome, returning non-ranged SummarizedExperiment" when I tried to use " library(tximeta) se=coldata2" . Here is my coldata2, its file.path worked properly image I am very confused so would you please help me to figure it out? plus, I've no idea why my "quant.sf" files, which are produced by salmon quant command, are kind of odd. Their head lines are as follows. Maybe that is the point? image Too much thanks!

mikelove commented 3 years ago

Can you take a look at #38 and confirm that your version of the transcriptome is in the set represented here:

https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.html#Pre-computed_checksums

mikelove commented 3 years ago

It looks like you quantified against chromosomes, not transcripts from that file.

Alexander-Suen commented 3 years ago

Oh, I see... A mistake... Thank you very much!