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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)task generates two data nodes: Transcript counts node contains NumReads which is the estimate of number of reads mapping to each transcript; Gene counts node contains the gene level reads which is the sum of all the reads from the corresponding transcripts from each gene.

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

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