We use both STAR and Salmon alignment methods in RNA-seq data analysis because they offer different strengths. STAR (Spliced Transcripts Alignment to a Reference) is an aligner designed to specifically address many of the challenges of RNA-seq data mapping, and it is able to accurately align reads to a reference genome. It's particularly effective in aligning reads that span splice junctions.

On the other hand, Salmon is a tool for quantifying transcript abundance from RNA-seq data. It doesn't align reads to the genome, but rather to a reference transcriptome. This can be faster and use less memory than aligning to the genome, especially for large genomes.

While both methods are useful, STAR is often seen as more accurate because it aligns reads to the reference genome, allowing it to account for factors like alternative splicing and novel transcripts. However, the choice between STAR and Salmon (or using both in combination) will depend on the specific needs of the project.