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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.

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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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