I am trying to use tximport on my read counts from kallisto. This is what Ive tried:

Txi_genebird <- tximport(path, type = "kallisto", tx2gene = Tx, txOut = FALSE countsFromAbundance = "lengthScaledTPM", ignoreTxVersion = TRUE, ignoreafterbar = TRUE) Error in .local(object, ...) : None of the transcripts in the quantification files are present in the first column of tx2gene. Check to see that you are using the same annotation for both.

Example IDs (file): [ENSTGUT00000000001, ENSTGUT00000000002, ENSTGUT00000000003, ...]

Example IDs (tx2gene): [ENSTGUT00000014203.2, ENSTGUT00000033741.1, ENSTGUT00000014202.2, ...]

This can sometimes (not always) be fixed using 'ignoreTxVersion' or 'ignoreAfterBar'.

I really don't know what else to do.. Any help appreciated!

I guess you have to remove the dot from the tx2gene file like tx2gene[,1] <- gsub("\\..*", "", tx2gene[,1]).

Edit: If I read the source code correctly (https://github.com/mikelove/tximport/blob/master/R/summarizeToGene.R#L41) then the ignoreTxVersion option acts only on the input files (so the abundance estimates and its rownames), but not on the tx2gene file itself, therefore what I suggest above should probably work.