Answers.Body: <p>Check your FASTQ headers - if they've been demultiplexed, the index barcodes can be found in the header. The barcodes are usually separated by a <code>+</code> in the comment part (second segment when the header is split by <code>&quot; &quot;</code> blank space) of the header. If you see a match to <code>[ATGC]{10}[+][ATGC]{10}</code> in the header, the first <code>[ATGC]{10}</code> is the I1 barcode and the second is the I2 barcode. You can use <code>FFFFFFFFFF</code> placeholder qual scores to generate &quot;fake&quot; I1 and I2 files and then use that with cellranger.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-27T18:00:10.387Z
Answers.Text: Thanks for your response. I'm not referring to the I1 & I2 files. I'm referring to feature barcoding technology using antibody capture (or potentially CRISPR). In the examples on the 10x website, they have separate fastq files for these, along with the gene expression fastq's
Answers.UserDisplayName: h3ab74
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-27T18:25:03.917Z
Answers.Text: I see, I apologize for the misunderstanding - I do not know how to help you with feature barcoding.
Answers.UserDisplayName: Ram RS
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Answers.CreationDate: 2023-03-27T15:38:22.457Z
Answers.LastActivityDate: 2023-03-27T15:38:22.457Z
Answers.UserDisplayName: Ram RS
Body: <p>I can't seem to find a clear answer to this question, so here it goes:</p>
  <p>I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody capture.</p>
  <p>There is a very useful <code>cellranger multi</code> command, which allows us to process both this data types in 'one go'.</p>
  <p>In order to run it one needs to generate a <code>csv</code> file a priori, such that <code>cellranger</code> is able to identify which files are pertinent to which file type - see this link:<a href="https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi" rel="nofollow noreferrer">https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi</a></p>
  <p>In the link above, with the example given under &quot;Example multi config CSVs&quot;, it seems as though there are separate <code>fastq</code> files for the feature barcode, versus for the actual gene expression samples. Whereas, in my case, I only have the standard <code>R1</code> and <code>R2</code> fastq files, which is creating some confusion as how to generate this file, and run cellranger.</p>
  <p>Now my question is, how does one run <code>cellranger multi</code> with feature barcoding should there only be the standard 2 <code>fastq</code> files? My understanding is that the feature barcode is usually in the <code>R2</code> read? Is this correct? Would I need to Demultiplex? I am completely lost as to how to proceed. If you know, could you please provide a short example of what your <code>csv</code> files would look like, should you not have separate <code>fastq</code> files for the feature barcode files?</p>
  <p>Thanks,</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-27T18:51:03.293Z
Comments.Text: How did you create your fastq files? If you've run `cellranger mkfastq` with the correct sample sheet, you should have got separate fastq files for each library: RNA-seq, VDJ-seq and feature barcode.
Comments.UserDisplayName: Cloudberry
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-27T19:30:17.793Z
Comments.Text: The fastq files were provided by the sequencing company.. We have 4 `fastq` files (R1,R2,I1,I2) for the GEX & VDJ sequencing, all run via 10x genomics. i.e. I don't have any bcl files, just the fastq's + aligned BAM's
Comments.UserDisplayName: h3ab74
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-28T20:27:09.603Z
Comments.Text: Before running cellranger multi you first need to demultiplex your fastq files to obtain separate files for each library. Unfortunately I've never demultiplexed fastq files so can't recommend any software.
Comments.UserDisplayName: Cloudberry
Tags: <scrnaseq><fastq><10x-genomics><cellranger><demultiplexing>
Title: Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)
ThreadText: # Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)
  
  (Asked by: username_0 on 2023-03-26)
  
  I can't seem to find a clear answer to this question, so here it goes:
  
  I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody capture.
  
  There is a very useful `cellranger multi` command, which allows us to process both this data types in 'one go'.
  
  In order to run it one needs to generate a `csv` file a priori, such that `cellranger` is able to identify which files are pertinent to which file type - see this link:<https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi>
  
  In the link above, with the example given under "Example multi config CSVs", it seems as though there are separate `fastq` files for the feature barcode, versus for the actual gene expression samples. Whereas, in my case, I only have the standard `R1` and `R2` fastq files, which is creating some confusion as how to generate this file, and run cellranger.
  
  Now my question is, how does one run `cellranger multi` with feature barcoding should there only be the standard 2 `fastq` files? My understanding is that the feature barcode is usually in the `R2` read? Is this correct? Would I need to Demultiplex? I am completely lost as to how to proceed. If you know, could you please provide a short example of what your `csv` files would look like, should you not have separate `fastq` files for the feature barcode files?
  
  Thanks,
  
  **Tags:** scrnaseq, fastq, 10x-genomics, cellranger, demultiplexing
  
  > **Comments:**
  > **username_1**: How did you create your fastq files? If you've run `cellranger mkfastq` with the correct sample sheet, you should have got separate fastq files for each library: RNA-seq, VDJ-seq and feature barcode.  
  > **username_0**: The fastq files were provided by the sequencing company.. We have 4 `fastq` files (R1,R2,I1,I2) for the GEX & VDJ sequencing, all run via 10x genomics. i.e. I don't have any bcl files, just the fastq's + aligned BAM's  
  > **username_1**: Before running cellranger multi you first need to demultiplex your fastq files to obtain separate files for each library. Unfortunately I've never demultiplexed fastq files so can't recommend any software.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-03-27. Score: 2
  
  Check your FASTQ headers - if they've been demultiplexed, the index barcodes can be found in the header. The barcodes are usually separated by a `+` in the comment part (second segment when the header is split by `" "` blank space) of the header. If you see a match to `[ATGC]{10}[+][ATGC]{10}` in the header, the first `[ATGC]{10}` is the I1 barcode and the second is the I2 barcode. You can use `FFFFFFFFFF` placeholder qual scores to generate "fake" I1 and I2 files and then use that with cellranger.
  
  > **Comments:**
  > **username_0**: Thanks for your response. I'm not referring to the I1 & I2 files. I'm referring to feature barcoding technology using antibody capture (or potentially CRISPR). In the examples on the 10x website, they have separate fastq files for these, along with the gene expression fastq's  
  > **username_2**: I see, I apologize for the misunderstanding - I do not know how to help you with feature barcoding.  
  
  ---
  
  