Question: tximport error with salmon version
gravatar for agetzler
15 months ago by
agetzler0 wrote:

Hi folks,

I am having some issues using tximport to make a counts object from salmon outputs to feed into DESEQ2. When I try to use the tximport function on a list of files corresponding to salmon outputs the resulting occurs:

> txi <- tximport(files[1], type="salmon", tx2gene=tx2gene)
reading in files with read_tsv
1 Error: package_version(minfo$salmon_version) >= "0.8.0" is not TRUE
> txi
Error: object 'txi' not found

I did, in fact, use a salmon version <= 0.8.0 (0.7.2 to be precise) as it was the most recent version available on my institution's HPC. Is there a work around or alternative package/ function to use for the lower version? Or does some additional functionality exist in salmon version 0.8.0 and higher that is required and thus I should just get that version installed and re run salmon. 

Thanks in advance for any help and suggestions,


Adam Getzler

Graduate Student 


ADD COMMENTlink modified 15 months ago by Michael Love19k • written 15 months ago by agetzler0
gravatar for Michael Love
15 months ago by
Michael Love19k
United States
Michael Love19k wrote:

Can you post sessionInfo()? 

And can you try dropInfReps=TRUE?

(Note also that it's typically easy to use the latest version of Salmon, by downloading the Linux binary)


ADD COMMENTlink written 15 months ago by Michael Love19k

Hi Michael,

Setting dropInfReps=TRUE solved the problem.



ADD REPLYlink written 15 months ago by agetzler0
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