Hi all,

I have salmon qunat.sf file when i tried to import i'm getting error

reading in files with read_tsv1 2 3 4 5 6 Error in tximport(files, type = "salmon", txOut = TRUE, countsFromAbundance = "scaledTPM") : all(c(abundanceCol, countsCol, lengthCol) %in% names(raw)) is not TRUE

salmon output looks like this.

Name    Length  EffectiveLength TPM     NumReads
ENST00000456328.2       1657    1619.661        0.000000        0.000

### R code
library(tximport)
txi <- tximport(files, type="salmon", txOut=TRUE,
                  countsFromAbundance="scaledTPM")

Can you please help mw with this?

Check the 6th file in files, it is probably corrupted, so the quant.sf file. What tximport does internally is to loop over all files and then (among other checks) makes sure that the essential columns are present. Here that is not the case for the 6th file as the error indicates.