I am trying to obtain human genes that overlap my mouse lncRNAs in human-mouse pairwise alignment.
For this purpose, I have been looking at mouse-human pairwise alignment in net format, but I can't fully understand what to do.
Is there no tool that can take in a net-formatted pairwise alignment and a bed file with genes of my interest in one species and spit out their counterparts for the other species based on the net file? I thought there should be such tools, but couldn't find one. And now I can't believe there is none for this purpose.
If you know how to do this, or know of tools for this, please let me know.