Hi,

is it possible to calculate gene-level count using transcript-quantification files generated by other software not currently supported by tximport?

Basically, I have transcript-level quantification files that were generated using STAR and I want to calculate gene-level abundance to be able to use DESeq2 downstream.

Best, Mohamed

Please note that STAR can calculate gene-level expression if you use the flag "--quantMode GeneCounts".

Yes, you can, there are the following arguments (from ?tximport)

geneIdCol - name of column with gene id. if missing, the tx2gene argument can be used txIdCol - name of column with tx id abundanceCol - name of column with abundances (e.g. TPM or FPKM) countsCol - name of column with estimated counts lengthCol - name of column with feature length information

You just have to specify these, and say type="none"