tximport error: vroom

Question

[Maxine]

when i trying import a list of salmon counts files quant.sf:

txi <- tximport(files=files, type="salmon", tx2gene=tx2gene[,c("refseq", "entrezid")], countsFromAbundance="lengthScaledTPM")

Rstudio throw me a error:

reading in files with read_tsv
1 Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names,  : 
  bad value

why did it happen?

Here are files and tx2gene look like:

> head(files)
                                                       cy201702 
"/Users/maxineliu/work/bufo/RNA/salmon/cy201702_quant/quant.sf" 
                                                       cy201802 
"/Users/maxineliu/work/bufo/RNA/salmon/cy201802_quant/quant.sf" 
                                                       cy201902 
"/Users/maxineliu/work/bufo/RNA/salmon/cy201902_quant/quant.sf" 
                                                       cy202302 
"/Users/maxineliu/work/bufo/RNA/salmon/cy202302_quant/quant.sf" 
                                                       cy202402 
"/Users/maxineliu/work/bufo/RNA/salmon/cy202402_quant/quant.sf" 
                                                       cy202502 
"/Users/maxineliu/work/bufo/RNA/salmon/cy202502_quant/quant.sf"

head(tx2gene[,c("refseq", "entrezid")])
          refseq  entrezid
1 XM_044268240.1 122946843
2 XM_044268241.1 122919300
3 XM_044268242.1 122919300
4 XM_044268243.1 122919300
5 XM_044268244.1 122919301
6 XM_044268245.1 122919299

[Kevin Blighe]

Cross-posted: https://support.bioconductor.org/p/9154550/

[Maxine]

yes, please go to the link above to discuss the issue.

Answer 1

[Trivas]

Which version of Salmon are you using? According to the tximport documentation, older versions of quant.sf files from Salmon have comments in the beginning. First, use head on one of your quant.sf files, and if that's the issue, the recommended way to get around this is to add the following to your tximport function:

importer = function(x) read_tsv(x, skip = 8)