salmon quantmerge giving fewer rows than expected


I have used salmon quant on a series of samples, and would like to merge the raw counts into a matrix for further processing. I have used a transcript-to-gene mapping file to get gene-level quantifications.

Each of my gene quantification outputs has 38,175 rows, but when I use quantmerge I only get 979 rows.

In quantmerge, I selected my gene quantification outputs and the NumReads column to merge.

I didn’t know whether to tick the Genes button or not. If I tick it, I get 0 rows in the quantmerge output.

Is there something I’m not understanding about this tool?

Could I use a column join instead to merge the data?