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.