<p>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?</p>

CC BY-SA 4.0
2022-08-22T05:25:30.750Z
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
CC BY-SA 4.0
2022-08-22T07:27:17.420Z
Yes, all right makes sense. Just another question. Are these reads per base pair or per insert?
Caterina
CC BY-SA 4.0
2022-08-22T17:40:43.537Z
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
<rna-seq><ngs><long-reads><pacbio>
Can multiplexing in Sequel II SMRTcells reduce the coverage?
# Can multiplexing in Sequel II SMRTcells reduce the coverage?

(Asked by: username_0 on 2022-08-20)

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?

**Tags:** rna-seq, ngs, long-reads, pacbio
> **Comments:**
> **username_1**: 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?  
> **username_0**: Yes, all right makes sense. Just another question. Are these reads per base pair or per insert?  
> **username_1**: 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.  

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## 0 answers

