I am trying to update my RNA-seq training materials to use the salmon tool for quantification rather than mapping and then counting.
My example data are Mouse, so I have downloaded the latest reference genomes from Ensembl and uploaded these to Galaxy:-
salmon works if I specify the fasta file from ensembl as my reference fasta. There is one row of output for each transcript
However, I would like to demonstrate how to obtain gene-level estimates by specifying a transcript to gene mapping. The tool suggests that a gtf file can be used, but when I use the gtf from Ensembl I still get the same number of transcripts in my “gene quantification” (suggesting that it cannot map the transcripts).
I have also created a tab-delimited from Biomart
|Transcript stable ID version||Gene stable ID|
By my salmon gene output still has all the transcripts.
Can anyone suggest where I am going wrong, or point me to some example fasta and transcript mapping files that work as expected?