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Question: tximport error with salmon version
0
gravatar for agetzler
4 months ago by
agetzler0
TSRI-FL
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 4 months ago by Michael Love14k • written 4 months ago by agetzler0
1
gravatar for Michael Love
4 months ago by
Michael Love14k
United States
Michael Love14k 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 4 months ago by Michael Love14k

Hi Michael,

Setting dropInfReps=TRUE solved the problem.

Thanks!

Adam 

ADD REPLYlink written 4 months ago by agetzler0
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