Get the read count per genomic bin for each 10x barcode (10x Genomics Single Cell Gene Expression protocol)

Question

[Nicola Casiraghi]

Given the BAM output of Cell Ranger (that contains all reads for each barcodes-cells) I want to count reads mapped to genomic bins for each barcode. I combined answer from How do I get the read counts for each barcode? with option -L as in:

samtools view -L bins.bed possorted_genome_bam.bam | grep CB:Z: | sed 's/.*CB:Z:\([ACGT]*\).*/\1/' | sort | uniq -c > reads_per_barcode

It works but the output read count is not for each target region, but overall across bins.

Can you point me to a possible way to get an output like:

bin1 read_count barcodeA
bin1 read_count barcodeB
bin1 read_count barcodeC
...
binN read_count barcodeA
binN read_count barcodeB
binN read_count barcodeC

thanks.

[swbarnes2]

I think you'll need to make a loop that goes through the lines of bins.bed one at a time