text: user4595: 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.
  
  user104: 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.
  
  user16818: 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.
  
original_text: 4595: <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>
   104: <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>
   16818: <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>
  