Answers.Body: <p>If you have UMIs, then cell/UMI/mapped transcript triplets should be collapsed into unique triplets.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-23T17:35:54.160Z
Answers.Text: I was looking at UMI Tools white list function; somehow it looks to me it consider all the reads for knee plot.
Answers.UserDisplayName: user3377241
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-23T09:10:19.370Z
Answers.LastActivityDate: 2023-12-23T09:10:19.370Z
Answers.UserDisplayName: gringer
Body: <p>I am trying to adapt combinatorial index reads with some modifications for long read sequencing; it's a custom approach, not a commercial kit.</p>
  <p>I have a question about using Knee Plot for identifying Barcode white list for non-10X data. While generating the Knee Plot barcode which barcode frequencies should be used: without collapsing PCR replicates to after collapsing PCR replicates?</p>
  <p>I have used UMI-Tools (<a href="https://umi-tools.readthedocs.io/en/latest/QUICK_START.html" rel="nofollow noreferrer">https://umi-tools.readthedocs.io/en/latest/QUICK_START.html</a>) and Pacbio groupdedup based approach. For the knee plot generation I used both collapsed and non-collapsed reads. Since its long reads and coverage is not great; bumps are not the perfect one but both inputs generate it. I am not sure which input I should consider to remove the backgrounds.</p>
  <p>Thanks</p>
  <p><strong>EDIT:</strong> <em>Can the down-voters please leave a note why they think this not a good query to ask?</em></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-01-02T18:10:03.780Z
Comments.Text: You're providing information as a trickle instead of providing all relevant information including what you've tried right in the post. One needs to read all comments to understand your position. Hence the downvote.
Comments.UserDisplayName: Ram RS
Tags: <scrnaseq><barcode><umi>
Title: Single Cell RNASeq Knee Plot - Collapsed vs Non-collapsed Reads
ThreadText: # Single Cell RNASeq Knee Plot - Collapsed vs Non-collapsed Reads
  
  (Asked by: username_0 on 2023-12-22)
  
  I am trying to adapt combinatorial index reads with some modifications for long read sequencing; it's a custom approach, not a commercial kit.
  
  I have a question about using Knee Plot for identifying Barcode white list for non-10X data. While generating the Knee Plot barcode which barcode frequencies should be used: without collapsing PCR replicates to after collapsing PCR replicates?
  
  I have used UMI-Tools (<https://umi-tools.readthedocs.io/en/latest/QUICK_START.html>) and Pacbio groupdedup based approach. For the knee plot generation I used both collapsed and non-collapsed reads. Since its long reads and coverage is not great; bumps are not the perfect one but both inputs generate it. I am not sure which input I should consider to remove the backgrounds.
  
  Thanks
  
  **EDIT:** *Can the down-voters please leave a note why they think this not a good query to ask?*
  
  **Tags:** scrnaseq, barcode, umi
  
  > **Comments:**
  > **username_1**: You're providing information as a trickle instead of providing all relevant information including what you've tried right in the post. One needs to read all comments to understand your position. Hence the downvote.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-12-23. Score: 0
  
  If you have UMIs, then cell/UMI/mapped transcript triplets should be collapsed into unique triplets.
  
  > **Comments:**
  > **username_0**: I was looking at UMI Tools white list function; somehow it looks to me it consider all the reads for knee plot.  
  
  ---
  
  