Hello all. I have sam/bam files with reads mapped to human genome from a RNA-seq experiment. I already tried bedtools
bedtools multicov [OPTIONS] -bams aln.1.bam aln.2.bam ... aln.n.bam -bed <bed/gff/vcf>, but it gave me the error 'Could not find indexes.'. Also, if the bedtools work, what shall be the output and how can I get a list with counts of reads mapping to genes? Any help is more than appreciated. Thank you.