Open blahah opened 9 years ago
Ooh, excellent points. I should definitely be careful to use a consistent terminology. And as for the gene–transcript quantification, I used some rather ugly simplification back when I did this, which consisted of quantifying gene expression and assigning it to the “canonical” transcript (the longest annotated CDS). Terrible, and I wouldn’t do it like that today, but in terms of codon usage it actually performs the task with very little bias.
Thanks, I’ll amend/explain that.
I was gonna read the rest of the thesis when I have time - let me know if this would be helpful now or if it's too soon to make useful comments.
I was actually going to submit immediately after BoG, so it’s definitely not too soon. The thesis isn’t extensively proofread yet but apart from that (and the lack of supplements) nothing much will change. If it helps you I can give you the reference library so you can compile the document — or you may prefer having the compiled document?
Great! Happy with either solution :)
In rna-seq.tex you have excellent discussion of various aspects of expression quantification. I think there are some missing pieces: