subjunc(1) on Linux
The text 7b36fb78cc15, as Debian 12 (Bookworm) shipped it.
toolkit for processing next-gen sequencing data
Flags it lists
-
--BAMinput -
--DPGapExt -
--DPMatch -
--SAMinput -
--SAMoutput -
--allJunctions -
--complexIndels -
--gtfAttr -
--gtfFeature -
--keepReadOrder -
--multiMapping -
--rg -
--rg-id -
--trim3 -
--trim5 -
-A -
-B -
-D -
-F -
-I -
-M -
-P -
-R -
-S -
-T -
-a -
-b -
-d -
-i -
-m -
-n -
-o -
-p -
-r -
-v