Salmon¹ is a method for quantifying transcript abundance from raw read sequence fastq files, it will generate transcript level count matrix as output.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5600148/

Running Salmon

Salmon will run on any FASTQ file input. 

• Click the data node containing your FASTQ files
• Click the Quantification section in the toolbox
• Click Salmon
• Choose Assembly and Aligner index on gene annotation model (Figure 1)

Salmon index can't be built on reference assembly, you need to provide transcript annotation file beforehand, the index will be built on transcript annotation model. For more information about adding aligner index based on annotation model,  see this chapter in library file management.

The output data node contains relative abundance of the transcripts in units of transcripts per million (TPM).

Note: If you want to perform differential analysis, you need to add offset to deal with 0 values.

References

1. Rob Patro, Geet Duggal, Michael Love, Rafeal A Irizarry, Carl Kingsford. Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference. Published online 2017 Mar 6. doi:10.1038/nmeth.4197