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16 months ago
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How can I separate a bam file into multiple bam files such that each bam file contains information for one cell using UMI-tools?
Assuming your data was processed by
cellranger
there should be a BAM fie withCB
tags in it. Using those to split the file would be the way to go.Some background info: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/bam#bam-bc-tags
There are some approaches outlined in the blog linked by @igor in this thread: scRNAseq: Split FASTQ into cell specific FASTQ Files