Scanning through all windows/aligns, not just bestTr. This adds a number of multimapping chimeras. With --chimMultimapNmax 50, all the old chimeric reads are present.
Scanning through all windows/aligns, not just bestTr. This adds a number of multimapping chimeras. With --chimMultimapNmax 50, all the old chimeric reads are present.

alexdobin/STAR,alexdobin/STAR,alexdobin/STAR,alexdobin/STAR