<p>Recently ran three separate single-cell experiments and sequenced them all using the <strong>10X platform</strong>. Each of the experiments involved <strong>GEX, FBC and VDJ</strong>. With the resulting BCL files, csv files with info on the layout (files with info on lane, sample and index) and feature refs csv, ran a Cell ranger pipeline that ran mkfastq, count and vdj functions. The pipeline generated the fastqs, <strong>broke down at the count stage (as described below)</strong>, but then successfully ran the vdj function.</p>
<p><em>Summary of the error:</em></p>
<p>Difficulty with running <code>Cellranger count</code>, where it has a difficulty automatically detecting the chemistry of a particular sample (GEX). This caused a failure in the <code>Cellranger count</code> function for this particular experiment. Please see the attached error messages along with the makeup of the directory that it is referring to.
If possible, I seek advice on finding where this error comes from, and how to avoid it in the future.</p>
<pre><code>Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries based on the R2 read mapping for sample GEX in ...
</code></pre>
<p>Where is this error is coming from? And how I would fix it/ avoid it in the future?</p>
<p>Also, will this affect my results as I continue with my single cell analysis? TCR?</p>
<p>I reran the count function for one of the experiments where this happened by specifying the chemistry using the --chemsitry parameter (would like to avoid in the future if that is better to do) and I am having difficulty with the resulting feature matrix files generated from the counts function. I am just wondering if that comes from the function or if it is an internal problem Ie my script that deals with the matrix files.</p>
<p>Any help/ advice would be greatly appreciated.</p>

CC BY-SA 4.0
2024-08-14T07:32:00.300Z
If you followed the 10x manual for the experiment then you should report this to the 10x technical support and let them figure it out. They're by experience quite helpful.
ATpoint
CC BY-SA 4.0
2024-08-14T13:08:06.737Z
I agree with ATpoint, it would be better to contact the manufacturer. They will be in a better position to help you out.
Karthik Nair
CC BY-SA 4.0
2024-08-14T14:46:12.100Z
Sounds good, thanks for your answers. I've contacted 10X support to see if they can help.
Odhran Casey
<single-cell><gene-expression><10x-genomics><cellranger>
10X Cellranger count - Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries based on the R2 read mapping for sample GEX in
# 10X Cellranger count - Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries based on the R2 read mapping for sample GEX in

(Asked by: username_0 on 2024-08-13)

Recently ran three separate single-cell experiments and sequenced them all using the 10X platform. Each of the experiments involved GEX, FBC and VDJ. With the resulting BCL files, csv files with info on the layout (files with info on lane, sample and index) and feature refs csv, ran a Cell ranger pipeline that ran mkfastq, count and vdj functions. The pipeline generated the fastqs, broke down at the count stage (as described below), but then successfully ran the vdj function.
Summary of the error:
Difficulty with running Cellranger count, where it has a difficulty automatically detecting the chemistry of a particular sample (GEX). This caused a failure in the Cellranger count function for this particular experiment. Please see the attached error messages along with the makeup of the directory that it is referring to.
If possible, I seek advice on finding where this error comes from, and how to avoid it in the future.
Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries based on the R2 read mapping for sample GEX in ...

Where is this error is coming from? And how I would fix it/ avoid it in the future?
Also, will this affect my results as I continue with my single cell analysis? TCR?
I reran the count function for one of the experiments where this happened by specifying the chemistry using the --chemsitry parameter (would like to avoid in the future if that is better to do) and I am having difficulty with the resulting feature matrix files generated from the counts function. I am just wondering if that comes from the function or if it is an internal problem Ie my script that deals with the matrix files.
Any help/ advice would be greatly appreciated.

**Tags:** single-cell, gene-expression, 10x-genomics, cellranger
> **Comments:**
> **username_1**: If you followed the 10x manual for the experiment then you should report this to the 10x technical support and let them figure it out. They're by experience quite helpful.  
> **username_2**: I agree with ATpoint, it would be better to contact the manufacturer. They will be in a better position to help you out.  
> **username_0**: Sounds good, thanks for your answers. I've contacted 10X support to see if they can help.  

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