Kallisto is really similar to salmon for "pseudo alignment", I ran it with about 8GB of RAM on human samples. I think the most demanding thing was building the RNA index, which you can get "pre-built" if you look around and probably could be run with a lot less. STAR is also really popular, but on the cusp of what is doable without moving to specialized hardware. When I played with it I could do human samples with about 32GB of RAM on a desktop after a lot of coaxing. You could move to AWS or university clusters at that point, which may be something you might be interested in anyways.
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22 months ago by
curious • 470
Computer requirements for RNAseq alignment
We Have The Minimum Of Everything Required For Bioinformatics Analysis; Why Do We Need More?
Minimum requirements for a laptop for RNA-seq
Thanks for the answer geno, and for the links AT.
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If quantifying gene expression and performing differential expression analysis, the requirements are very small, depending on the method. See the small experiment Bioinformatics on a Rock64. However, I don't know if the same machine is sufficient to perform all steps, as the post doesn't make it clear if the human transcriptome index was built by the same Rock64, or built externally by a more powerful computer.