Answers.Body: <p>I'm not entirely clear on your question, but if it is about the 10X 3' vs. 5' solutions then either can be used to sequence PBMCs. The principle difference is that 3' captures the 3' end of the transcript and 5' captures the 5' end. The differences are more important for multi-modal single cell data, e.g. only the 5' can be combined with VDJ sequencing and for CITE-seq, different antibody panels are compatible with each tech. There are also some more subtle differences and technical nuances.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-01-18T19:45:08.060Z
Answers.LastActivityDate: 2022-01-18T19:45:08.060Z
Answers.UserDisplayName: Chris_Rands
Answers.Body: <p>It depends on the task. If you want to recover TCR and BCR repertoires along with gene expression - 5' is a must. Also, for an overview repertoire analysis you dont even have to perform target enrichment and use 5' RNA-seq daata to directly recover the repertoire.</p>
  <p>Its easy to do with MiXCR software in one line command:</p>
  <pre><code>mixcr analyze 10x-5gex-full-length \
   --species hsa \
   sample_R1.fastq.gz \
   sample_R2.fastq.gz \
   sample_result
  </code></pre>
  <p>Though MiXCR currently only supports repertoire analysis it will also support gene expression soon.</p>
  <p>More on that here:
  <a href="https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#10xgenomics" rel="nofollow noreferrer">https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#10xgenomics</a></p>
  <p>Disclaimer: I work for the company that develops MiXCR.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-26T00:40:30.550Z
Answers.Text: Just to mention that it is possible Mark Izaelson is employed by MiLaboratories. However, it is great that the post was edited to describe the algorithm.
Answers.UserDisplayName: M__
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Answers.LastEditDate: 2023-01-27T10:59:16.820Z
Answers.UserDisplayName: Mark Izraelson
Body: <p>I have PBMCs of some patients who have recovered from cancer, and I want to look at their immune landscapes.</p>
  <p>I got confused when looking at available kits: can I use 5' end kits from 10x instead of 3' end based?</p>
  <p>I tried to search for information on this, but I am not clear if 5' can substitute for 3' or if they are just too different.</p>
  
Tags: <scrnaseq><single-cell><10x>
Title: Can 5' end 10x be used instead of 3' end
ThreadText: # Can 5' end 10x be used instead of 3' end
  
  (Asked by: username_0 on 2022-01-18)
  
  I have PBMCs of some patients who have recovered from cancer, and I want to look at their immune landscapes.
  
  I got confused when looking at available kits: can I use 5' end kits from 10x instead of 3' end based?
  
  I tried to search for information on this, but I am not clear if 5' can substitute for 3' or if they are just too different.
  
  **Tags:** scrnaseq, single-cell, 10x
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2022-01-18. Score: 3 | Accepted answer
  
  I'm not entirely clear on your question, but if it is about the 10X 3' vs. 5' solutions then either can be used to sequence PBMCs. The principle difference is that 3' captures the 3' end of the transcript and 5' captures the 5' end. The differences are more important for multi-modal single cell data, e.g. only the 5' can be combined with VDJ sequencing and for CITE-seq, different antibody panels are compatible with each tech. There are also some more subtle differences and technical nuances.
  
  
  ---
  
  ### Answer by username_2 on 2023-01-25. Score: 3
  
  It depends on the task. If you want to recover TCR and BCR repertoires along with gene expression - 5' is a must. Also, for an overview repertoire analysis you dont even have to perform target enrichment and use 5' RNA-seq daata to directly recover the repertoire.
  
  Its easy to do with MiXCR software in one line command:
  
  ```
  mixcr analyze 10x-5gex-full-length \
   --species hsa \
   sample_R1.fastq.gz \
   sample_R2.fastq.gz \
   sample_result
  
  ```
  
  Though MiXCR currently only supports repertoire analysis it will also support gene expression soon.
  
  More on that here:
  <https://docs.milaboratories.com/mixcr/reference/overview-built-in-presets/#10xgenomics>
  
  Disclaimer: I work for the company that develops MiXCR.
  
  > **Comments:**
  > **username_3**: Just to mention that it is possible Mark Izaelson is employed by MiLaboratories. However, it is great that the post was edited to describe the algorithm.  
  
  ---
  
  