Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-01T17:59:01.070Z
Answers.LastActivityDate: 2018-06-01T17:59:01.070Z
Answers.UserDisplayName: swbarnes2
Body: <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>
  
Tags: <rna-seq><scrnaseq><10x-genomics>
Title: How to search a specific sequence in BAM files for 10X experiment
ThreadText: # How to search a specific sequence in BAM files for 10X experiment
  
  (Asked by: username_0 on 2018-06-01)
  
  I have to search a specific sequence in a set of cells (> 1k cells) from a single-cell experiment done with [10X genomics](https://www.10xgenomics.com/).
  
  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.
  
  **Tags:** rna-seq, scrnaseq, 10x-genomics
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2018-06-01. Score: 2 | Accepted answer
  
  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>
  
  
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