Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-14T07:32:00.300Z
Comments.Text: 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.
Comments.UserDisplayName: ATpoint
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-14T13:08:06.737Z
Comments.Text: I agree with ATpoint, it would be better to contact the manufacturer. They will be in a better position to help you out.
Comments.UserDisplayName: Karthik Nair
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-14T14:46:12.100Z
Comments.Text: Sounds good, thanks for your answers. I've contacted 10X support to see if they can help.
Comments.UserDisplayName: Odhran Casey
Tags: <single-cell><gene-expression><10x-genomics><cellranger>
Title: 10X Cellranger count - Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries based on the R2 read mapping for sample GEX in
ThreadText: # 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 username_1, 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.  
  
  ---
  
  ## 0 answers
  
  