Just to verify: You are running the newest versions of TopHat and other programs that are currently available?
Can you try an index-only run of TopHat to see if the GTF file works
Can you try an index-only run of TopHat to see if the GTF file works
Code:
$ tophat2 -G gencode.v20.2wayconspseudos.gtf \ --transcriptome-index=MSCd0Adip-12/transcriptome GRCh38
Comment