Using igvtools count with bam anf bam.bai files

Question

[Bella_p]

Hi all,

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!!!

Answer 1

[h.mon]

The .bam file contains the mapping information (hence the information that will be used for counting and plotting), the .bam.bai is a index for the corresponding position-sorted .bam. The .bam.bai does not contain any information about read mapping, but it is often required so the .bam can be used by downstream tools.

[Bella_p]

Thanks! Is it needed for igvtools count? or IGV visualization? and how is it different from .bed file?

[h.mon]

Yes, it is needed, but I believe if IGV does not find the .bam.bai, it will automatically index the .bam for you.