<p>I have solve this problem, cause the combined barcode is differernt from the common 10x barcode. when mapping the genome, need to add-- chemistry ARC-v1 when cellranger count.</p>

CC BY-SA 4.0
2023-11-01T16:44:20.577Z
ARC-v1 means this was done using a multiomic kit. From `cellranger count --help` "To analyze the GEX portion of multiome data, chemistry must be set to 'ARC-v1'; 'ARC-v1' chemistry cannot be autodetected"
nico
CC BY-SA 4.0
2022-04-06T06:10:30.023Z
Excuse me, how do you determine the required chemistry?
JY_sea
CC BY-SA 4.0
2021-12-13T03:24:41.060Z
2021-12-13T03:24:41.060Z
ciwei
<p>Answer from @maximilian-press, converted from comments:</p>
<blockquote>
<p>I can't comment on 10X data specifically, however, I suggest writing a
simple script or command that counts the frequency of each barcode,
and reports back the N (10? 20? 100?) most frequent ones, which will
allow you to investigate in more detail. This is what I have done in
the case of suspected bardode swaps or reverse complement issues.</p>
</blockquote>

CC BY-SA 4.0
2021-12-12T23:57:07.210Z
2021-12-12T23:57:07.210Z
gringer
<p>I am testing a 10x fastq dataset , but cellranger count complains &quot;An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input&quot;, I have tried all the chemistry recommendation codes on the 10x genomics website, and I still get the same result, how can I solve this problem, thanks.</p>
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<a href="https://i.sstatic.net/FChZu.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/FChZu.jpg" alt="enter image description here" /></a></p>

CC BY-SA 4.0
2021-12-12T14:03:43.973Z
It is difficult to provide an answer when the question does not include what the input is, what command was run, ... I can only suggest to use the `--chemistry=auto` option of `cellranger count`.
haci
CC BY-SA 4.0
2021-12-12T22:44:41.660Z
What does the quality look like on those reads?  If this is 10XGenomics library, they should be able to help your troubleshoot.
swbarnes2
CC BY-SA 4.0
2021-12-12T23:41:42.660Z
Could you please give a few more details about the nature of this project? Are you sure this is a single-cell dataset (I'm aware that 10X do other non-single-cell things as well)? Showing the first few lines of header from the fastq files can be very helpful to work out the structure of the experiment.
gringer
CC BY-SA 4.0
2021-12-13T21:01:42.213Z
how were your fastqs generated? and how are they named?
Chris_Rands
CC BY-SA 4.0
2023-09-02T13:34:08.813Z
Thanks @ciwei for providing your answer. Could you kindly check the "accept" box for your answer? This does help site statistics
M__
<single-cell><fastq>
10X low rate of correct barcodes was observed for the candidate chemistry choices for the input
# 10X low rate of correct barcodes was observed for the candidate chemistry choices for the input

(Asked by: username_0 on 2021-12-12)

I am testing a 10x fastq dataset , but cellranger count complains "An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input", I have tried all the chemistry recommendation codes on the 10x genomics website, and I still get the same result, how can I solve this problem, thanks.

[![enter image description here](https://i.sstatic.net/Ra0XA.png)](https://i.sstatic.net/Ra0XA.png)
[![enter image description here](https://i.sstatic.net/FChZu.jpg)](https://i.sstatic.net/FChZu.jpg)

**Tags:** single-cell, fastq
> **Comments:**
> **username_1**: It is difficult to provide an answer when the question does not include what the input is, what command was run, ... I can only suggest to use the `--chemistry=auto` option of `cellranger count`.  
> **username_2**: What does the quality look like on those reads?  If this is 10XGenomics library, they should be able to help your troubleshoot.  
> **username_3**: Could you please give a few more details about the nature of this project? Are you sure this is a single-cell dataset (I'm aware that 10X do other non-single-cell things as well)? Showing the first few lines of header from the fastq files can be very helpful to work out the structure of the experiment.  
> **username_4**: how were your fastqs generated? and how are they named?  
> **username_5**: Thanks @ciwei for providing your answer. Could you kindly check the "accept" box for your answer? This does help site statistics  

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## 2 answers

### Answer by username_0 on 2021-12-13. Score: 2

I have solve this problem, cause the combined barcode is differernt from the common 10x barcode. when mapping the genome, need to add-- chemistry ARC-v1 when cellranger count.

> **Comments:**
> **username_7**: Excuse me, how do you determine the required chemistry?  
> **username_6**: ARC-v1 means this was done using a multiomic kit. From `cellranger count --help` "To analyze the GEX portion of multiome data, chemistry must be set to 'ARC-v1'; 'ARC-v1' chemistry cannot be autodetected"  

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### Answer by username_3 on 2021-12-12. Score: 0

Answer from @maximilian-press, converted from comments:

> I can't comment on 10X data specifically, however, I suggest writing a
> simple script or command that counts the frequency of each barcode,
> and reports back the N (10? 20? 100?) most frequent ones, which will
> allow you to investigate in more detail. This is what I have done in
> the case of suspected bardode swaps or reverse complement issues.


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