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