How to combine the alignment result of BWA and STAR? about ricpipe HOT 3 CLOSED

I'm also not sure why you need to use STAR to align first and unmapped reads were aligned again with bwa.

from ricpipe.

Because STAR tolerates reads with a mismatch at the spliced junction sites (i.e., linear mapping)
BUT has a low tolerate rate for reads with a mismatch at the chimeric junction sites (i.e., invert mapping). For this part of reads, I used bwa to further detect chimeric junctions.

For Supplementary Alignment,

from ricpipe.

Thank you !
In my result, there is a cluster that the left arm overlaps the right arm.
"chr12 8053387 8053492 chr12 8053466 8053492 FianlCluster_57"
Does this mean there is something wrong with my program?

from ricpipe.