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.