Hi,
Currently, I am doing RNA-seq analyses on a non-reference species. I used Kallisto, Salmon, and RSEM for the quantification of reads and found similar results between the three tools, though not exactly the same. To understand the differences between these tools, I discovered that RSEM performs alignment of reads, Salmon uses a mapping-based mode, and Kallisto uses pseudoalignment of reads. Can anyone help me figure out the differences between these three tools and the methods of alignment mentioned?
It's nice that you've gone ahead and done some analysis of these results and their differences on your data yourself. These more general questions you raise have already been discussed on this site. Likewise, there are also papers addressing these questions, which are worth reading if you feel the difference you observe may be biologically relevant in your context.
Thank you so much for your response. The two links are really helpful. I appreciate it. Have a nice day!
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