I've been requested how to make a plot like this, which is from an ATAC-Seq methods paper (Buenrostro, J.D., et al. doi: 10.1002/0471142727.mb2129s109) of RNA-Seq Data I'm not sure how I can get the insert size and then the normalized read density. I've tried rseqc's insertion_profile.py but there are bugs in that script so I can't use it.
How can I go about making getting this data from fastq or aligned bam files? EDIT: