I have the StringTie output files and need to run DGE using DESeq2. I ran the following code:
tx2gene <- tmp[, c("t_name", "gene_name")]
With that I was able to extract t_name and gene_name columns. But this was for only one sample.
However, when I execute
txi <- tximport(files, type = "stringtie", tx2gene = tx2gene) I got an error.
What does "files" mean in this last code?
I suppose files refer to t_data.ctab files (one for each sample), is that right? Nevertheless, in the tx2gene there is only one sample processed.
How I can merge the "t_data.ctab" files to get the data matrix needed for DESeq2?
May you please provide the detailed script to do so?