Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-11-01T16:44:20.577Z
Answers.Text: 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"
Answers.UserDisplayName: nico
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Answers.CreationDate: 2022-04-06T06:10:30.023Z
Answers.Text: Excuse me, how do you determine the required chemistry?
Answers.UserDisplayName: JY_sea
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Answers.CreationDate: 2021-12-13T03:24:41.060Z
Answers.LastActivityDate: 2021-12-13T03:24:41.060Z
Answers.UserDisplayName: ciwei
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-12-12T23:57:07.210Z
Answers.LastActivityDate: 2021-12-12T23:57:07.210Z
Answers.UserDisplayName: gringer
Body: <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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Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-12T14:03:43.973Z
Comments.Text: 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`.
Comments.UserDisplayName: haci
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-12T22:44:41.660Z
Comments.Text: What does the quality look like on those reads?  If this is 10XGenomics library, they should be able to help your troubleshoot.
Comments.UserDisplayName: swbarnes2
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-12T23:41:42.660Z
Comments.Text: 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.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-12-13T21:01:42.213Z
Comments.Text: how were your fastqs generated? and how are they named?
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-02T13:34:08.813Z
Comments.Text: Thanks @ciwei for providing your answer. Could you kindly check the "accept" box for your answer? This does help site statistics
Comments.UserDisplayName: M__
Tags: <single-cell><fastq>
Title: 10X low rate of correct barcodes was observed for the candidate chemistry choices for the input
ThreadText: # 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 @username_0 for providing your answer. Could you kindly check the "accept" box for your answer? This does help site statistics  
  
  ---
  
  ## 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"  
  
  ---
  
  ### 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.
  
  
  ---
  
  