I'm working through the example data set for LeafCutter and the documentation mentions "split reads":
This will cluster together the introns fond [sic] in the junc files listed in test_juncfiles.txt, requiring 50 split reads supporting each cluster and allowing introns of up to 500kb.
Searching "split reads" on Google yielded few results, and the results I did find were hard for me understand,
Chimeric reads occur when one sequencing read aligns to two distinct portions of the genome with little or no overlap. Chimeric reads are indicative of structural variation. Chimeric reads are also called split reads.
One sequencing read aligns to two distinct portions of the genome, but then with little or no overlap? Isn't that a self-contradiction?
I can more or less deduce what "intron clusters" are but I figured I might as well try to solicit a more formal definition. I know what introns are and I can figure what it means to cluster them together. I guess I just want to know what split reads and intron clusters mean in the context of working out the example data for LeafCutter.