How do determine the ratio of mRNA:rRNA:ncRNA in an RNA-seq dataset?
I have an RNAseq data set and I would like to know how much of what maps to the human genome is either mRNA, rRNA (didn't deplete this in my experimental design), or ncRNA.
Is there either a script that already does this or genome assemblies for each RNA sub class to which I can align my dataset?
Thank you!
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Take a look in rfam.xfam.org ;)