text: user1771: I have to search a specific sequence in a set of cells (> 1k cells) from a single-cell experiment done with 10X genomics.
  As input file I have a single bam file, and 24 fastqs, therefore each file contains information about several cells. How can I search for a specific sequence and underpin which single cells have it?
  I should be able to search for a specific sequence in a bam using samtools, etc. But the issue here is how to demultiplex the data from different cells to understand which cell provide the sequence.
  
  user2388: The bam file has bam tags which say what reads belong to what cells.
  https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/bam
  
original_text: 1771: <p>I have to search a specific sequence in a set of cells (> 1k cells) from a single-cell experiment done with <a href="https://www.10xgenomics.com/" rel="nofollow noreferrer">10X genomics</a>.</p>
  
  <p>As input file I have a single bam file, and 24 fastqs, therefore each file contains information about several cells. How can I search for a specific sequence and underpin which single cells have it?</p>
  
  <p>I should be able to search for a specific sequence in a bam using samtools, etc. But the issue here is how to demultiplex the data from different cells to understand which cell provide the sequence.</p>
   2388: <p>The bam file has bam tags which say what reads belong to what cells.</p>
  
  <p><a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/bam" rel="nofollow noreferrer">https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/bam</a></p>
  