<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>

CC BY-SA 4.0
2018-06-01T17:59:01.070Z
2018-06-01T17:59:01.070Z
swbarnes2
<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>

<rna-seq><scrnaseq><10x-genomics>
How to search a specific sequence in BAM files for 10X experiment
# 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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