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I would like to have high depth of coverage of the transcriptome, but I need to analyze several tissues. I was suggested to pool all 5 tissue samples in same SMRT 8M cell. Will this result in a smaller coverage when compared to non-multiplex version?

Caterina
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  • Well, necessarily multiplexing reduces coverage of each sample. 1M reads / 1 sample > 1M reads / 5 samples (assuming even coverage). Is this what you are asking? – Maximilian Press Aug 22 '22 at 05:25
  • Yes, all right makes sense. Just another question. Are these reads per base pair or per insert? – Caterina Aug 22 '22 at 07:27
  • A little unsure what that's asking, but if I understand you to mean library inserts, it will be reads per insert (species of DNA in the library). That should be strongly correlated to genome/transcriptome bases covered, so unless you have some rather wacky insert sizes it will imply reads per base as well. – Maximilian Press Aug 22 '22 at 17:40

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