I hope all is well. I have a quick question about my STAR -> stringtie -> cuffcompare workflow. I found it odd that there were no frags of type "j" when I typed the following:

$ cut -f4 ${sample}.tracking | sort | uniq -c
   3864 =
  14532 c
  27422 e
  25872 i
   8018 o
   2031 p
  21619 u
     19 x

Has anyone encountered this before? It seems very odd that there are 0 novel isoforms. I am using the Rnor_6.0 gtf file, which contains splicing annotations.

Your help would be appreciated. Thanks!