I'm pretty new to RNAseq, and I have been following this tutorial to get my data RNAseq data DESeq2 compatible (https://bioconductor.github.io/BiocWorkshops/rna-seq-data-analysis-with-deseq2.html). I get my sf file via Salmon. However, I'm getting this error once I try to call the tximport command:
txi = tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion= TRUE, ignoreAfterBar=TRUE)
"Error in summarizeToGene(txi, tx2gene, varReduce, ignoreTxVersion, ignoreAfterBar, : 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): [ebi, ...] Example IDs (tx2gene): [ENST00000456328.2, ENST00000450305.2, ENST00000473358.1, ...] This can sometimes (not always) be fixed using 'ignoreTxVersion' or 'ignoreAfterBar'."
I've looked at previously answered questions, and the most common suggestion was to put ignoreTxVersion=TRUE or ignoreAfterBar = TRUE. I have tried both, but I am still getting the same error. Not too sure what to do. Any suggestions?