DNAseq data and trying to get the read
counts per chromosome arm. but I do not know the correct way. shall I align to every chromosome separately or the whole genome? how can I count the reads per chromosome arm? I mean what tool can I use for this goal?
get a bed for each q/p for each chromosome, eg. see Programmatically convert cytoband location to genomic coordinates
then for each bed record, use
samtools view -c to count the reads.