IsoformSwitchAnalyzR - "longer object length is not a multiple of shorter object length"

Hello! I am trying to use this tool to compare differences in two conditions across three samples. I get the following error message when trying to import my data:

“reading in files with read_tsv
1 2 Error in tximport::tximport(files = localFiles, type = tolower(dataAnalyed$orign), :
all(txId == raw[[txIdCol]]) is not TRUE
Calls: importIsoformExpression → → stopifnot
Warning message:
In txId == raw[[txIdCol]] :
longer object length is not a multiple of shorter object length”

The error message suggests that I have duplicate input datasets, but I do not - they’re three different inputs per condition.

I performed transcriptome assembly using the following tutorial and I don’t know if this is part of the issue?

My history:

Any help is greatly appreciated!

Hi @Margaret_M

Notice how the transcripts are named in the Stringtie files – they are using the default transcript names generated for novel transcripts by that tool. These instead need to match up with the reference annotation’s transcript_id attributes and the >lines in the transcript fasta.

It looks like you missed a step that consolidates that data: Stringtie merge. Scroll up in the tutorial to find it.

Thank you very much. I have a new error, but this at least solves that one