This is a great tutorial, thank you! One suggestion - in the step where you're detecting the ribosomal protein transcript content of each library, I think you should actually be using a list of ribosomal RNA and tRNA genes. These non-coding RNAs are in abundance in the cytoplasm and are considered contaminants in gene expression libraries, whereas ribosomal protein transcript are not. I don't have a direct source for this list, but you can compile one pretty easily.
Chris
This is a great tutorial, thank you! One suggestion - in the step where you're detecting the ribosomal protein transcript content of each library, I think you should actually be using a list of ribosomal RNA and tRNA genes. These non-coding RNAs are in abundance in the cytoplasm and are considered contaminants in gene expression libraries, whereas ribosomal protein transcript are not. I don't have a direct source for this list, but you can compile one pretty easily.
Chris