Separating a bam file into multiple bam files

How can I separate a bam file into multiple bam files such that each bam file contains information for one cell using UMI-tools?

bam scrna-seq umi-tools

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updated 3.3 years ago by Ram 4.5K • | written 3.7 years ago by Researcher 3

Assuming your data was processed by cellranger there should be a BAM fie with CB 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

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written 3.7 years ago by GenoMax 16K

1 answer

10x provides an unsupported tool for this: https://github.com/10XGenomics/subset-bam You will need a list of cell barcodes.

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written 3.7 years ago by GenoMax 16K

Thank you. I appreciate your help. I have not tried your answer yet because I found an R package, Sierra that seems to have a function for splitting a bam file into multiple bam files for every cell, "https://rdrr.io/github/VCCRI/Sierra/man/SplitBam.html". Have you ever tried this?

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written 3.7 years ago by Researcher 3

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