I'm a beginner with using igv, and I have .bam file and it's .bam.bai file, that I created using samtools index. Is igvtools count accepts both files (bam and bam.bai)? according to the wesbite: "Supported input file formats are: .sam, .bam, .aligned, .psl, .pslx, and .bed." can't see anything about bam.bai...maybe I'm confusing with IGV visualization? Can someone please explain it to me? I think I'd like to use igvtools count to get the counting hits in my Chip-seq experiment and to use IGV visualization to visualize it. also, the output for igvtools count is .bed file? then I'll be able to use it for IGV visualization?
Appreciate any help!!!