I have control and treated RNASeq samples. I want to use them for metatranscriptomics analysis.
I have generated .daa file using SAMSA 2 package.
I have meganized the .daa file using MEGAN 6 software.
I would like compare the above 2 datasets.
In the compare panel, should I use absolute reads or normalized reads? Which would be a better analysis?
The normalized counts is reducing to 4 lakhs whereas the absolute reads is upto 32 lakhs
The normalized comparison normalizes to the smallest given count. If you don’t normalize, then the “species (or taxa) richness” of your samples with be biased, with the smaller samples appearing less species-rich due to the fact that more low abundance taxa are missing.
In continuation of the above topic, I was wondering if it would make sense to export the read count ( now I have imported the normalised read count) and use these for deseq2 or edgeR analysis? Or import absolute read count and then use that for edgeR or Deseq2 analysis? If I use the normalized read count am I re normalizing the reads? Do let me know how I should go about if I would like to do some comparative studies. Thank you.