Can anyone guide me on how to use rnaseqcomp for own data when we don't have reference genes
I am comparing kallisto and rsem - quantificationtool comparision.
Not helping with your question but you better compare recent tools such as kallisto to salmon rather than rsem which is quite old by now. For differences between salmon and rsem see e.g. Main difference between RSEM and k-mer based quantification methods. You should also check the papers of these tools as they contain some benchmarkings.
RSEM is a widely used tool that produces good results by various benchmarks. On the other hand, a comparison between kallisto and Salmon is pointless because they have been shown in multiple comparisons to produce near identical results. For a recent reference for both these points see https://www.biorxiv.org/content/10.1101/698605v1.abstract
thank you for your comments.
I have seen many articles and found rsem is a better tool, I just want to see the difference in my data. I found a tool rnaseqcomp but it comes with the incomplete manual.
after that, I also want to compare common and specific DE genes of the tools
Lpacther I think I have read almost all of your articles :)
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