Map and count sequencing reads to genomic regions
It requires 6 positional arguments to run:
- Path to flowcell
- A path to a bedfile with the reference genomic regions
- A FASTA file with the adapters to be trimmed
- Path to the reference genome
- MAPQ value
- The SAM flag
-fto filter the BAM file
It returns a tab-delimted table with counts per genomic region for each sample