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!