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The article that you link to clarifies in the methods section that there are two different extraction protocols employed, one for 16S information (probably DNA extraction) and one for total RNA. In fact, the 16S data comes from a previous publication. I would suggest following the recommendations in these methods sections with regard to kits, sample ...


pyrpipe claims to be a one-stop python library for RNA-seq analysis. Here is an illustration from their paper: Furthermore, I would like to draw attention to ENCODE's official RNA-seq pipeline, which is actively maintained on ENCODE-DCC's GitHub repository.

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