Hey all,

I am trying to visualize sample_aligments.bam from cellranger, which they described as

Indexed BAM file containing position-sorted reads aligned to the genome and transcriptome, as well as unaligned reads, annotated with barcode information.

I use IGV to visualize trying to see my knockout efficiency. But it is all blank. Like this:

And then I went to the whole genome alignment,

It's so weird, since the seurat object converted from outputs of cellranger looks fine and seems infallible. Maybe single cell data is too sparse to visualize? Maybe I have done something wrong?

Could you help me figuring out this?

Thank you so much!