I have next to zero experience with D. melanogaster biology, but I've processed quite a few mouse and human experiments.As a task for students I've chosen D.melanogaster RNA-seq experiment - since the genome is so much smaller and I figures it would work faster on their machines. Here's the experiment I've used - it's a cell line:
I've aligned the experiment to dm6 reference with hisat2 and visualized the BAM with IGV. What I can't understand is why do all of the variants look homozygous? Is that normal? Is that because they are very inbred?
Thank you for any input.