Hi,
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?
Thanks,
Mark