I have have tx2gene files that are output from Orthofinder. Kallisto abundances were generated from for two different assemblies from different tissues. Ultimately I am hoping to use edgeR TMM means to get a normalization factor across the tissues.

I was able to upload the abundance files according to the vignette https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Import_transcript-level_estimates

I used cat to merge the two tx2gene files so that the transcript IDs from both tissues were included in the map, however when I ran the following code I got the error because tximport requires that the tx ids are in the same order for the abundance files and the tx2gene map. Is there a way to deal with this issue where I have separate tx2gene maps for each sample using tximport?

Thank you so much!!

txi.kallisto.tsv <- tximport(files, type = "kallisto", tx2gene = tx2gene)

#tximport is throwing the error 
1 2 Error in tximport(files, type = "kallisto", tx2gene = tx2gene) :
  all(txId == raw[[txIdCol]]) is not TRUE
In addition: Warning message:
In txId == raw[[txIdCol]] :
  longer object length is not a multiple of shorter object length

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

Missed this but followed up on the later post:

tximport error: all(txId == raw[[txIdCol]]) is not TRUE