I generated TPM counts from fastq data using salmon. This leaves me with the NM_transcript IDs. I would like to generate the gene symbols from the transcript IDs . Biomart does not recognize transcripts, NCBI Datasets produces an error when I run the entire transcriptome. I have been exploring tximport and tximeta, however, I have run into numerous issues particularly with tximeta not detecting my ref file. Any advice would be greatly appreciated.
Update: I have txiimport and tximeta now running, however they create S4 objects and I am unsure how to make these readable