Hi @Egle,
Salmon works on a reference transcriptome. You don’t need alignments: Salmon takes FASTQ files. Because of alternative splicing, you need a file with transcript to genes map. I had less issues with a tabular transcript-to-genes map file. Here is my old history with Salmon: Galaxy | Australia | Published History | Transcript quantification with Salmon 2018/06/08
You may also consider a traditional approach: mapping with HiSAT2 and read counting with featureCounts. GTN provides several detailed tutorials for this approach.
Kind regards,
Igor
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