Entering edit mode
I am attempting to do differential gene expression analysis on kallisto aligned data from the TOIL project. I want to use tximport to summarize the transcript level data to the gene level. The format of the abundance and count files is a matrix with ENST transcript IDs as rows and sample names as columns. I am wondering how I can use tximport to summarize these transcripts to the gene level given that the data is not in the classic kallisto format. If it is not possible to use tximport, how should I summarize the transcript IDs to gene names?
recount 2 does not use kallisto, does it? And recount does offer genelevel counts, so what's the point?
Sorry, I misspoke. The data was from the TOIL project and was aligned using kallisto. It was accessed from the UCSC XENA browser. I updated my post with these corrections.