Convert 10x single cell RNA-seq bam file to bulk RNA-seq bam file

Question

[krc3004]

Hi,

Given a sorted bam file from standard 10x cell ranger output, i.e. from https://support.10xgenomics.com/single-cell-vdj/datasets/4.0.0/sc5p_v1p1_hs_PBMC_1k, I am wondering if it's possible to convert this scRNA-seq bam file to a bulk RNA-seq ("pseudo-bulk") bam file, e.g. combining reads across all cell barcodes in the bam file?

I imagine there is a way to do this using samtools, but could not find any examples. Any help would be much appreciated. Thanks!

Answer 1

[rpolicastro]

It's a normal bam file, just with a few extra tags with cell barcodes and such. You can read more about the tags on the 10X website here. Because there is nothing special about it, you can use any feature counting software designed for RNA-seq, such as Subread or HTSeq.