<p>If you have UMIs, then cell/UMI/mapped transcript triplets should be collapsed into unique triplets.</p>

CC BY-SA 4.0
2023-12-23T17:35:54.160Z
I was looking at UMI Tools white list function; somehow it looks to me it consider all the reads for knee plot.
user3377241
CC BY-SA 4.0
2023-12-23T09:10:19.370Z
2023-12-23T09:10:19.370Z
gringer
<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>

CC BY-SA 4.0
2024-01-02T18:10:03.780Z
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.
Ram RS
<scrnaseq><barcode><umi>
Single Cell RNASeq Knee Plot - Collapsed vs Non-collapsed Reads
# 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.  

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## 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.  

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