Cufflinks has an option of -M <mask.(gtf/gff)>, which could be used to mask certain transcripts. However, I still found many transcripts having some levels of FPKM after masking, some even reach ~200 Besides, the file "skipped.gtf" in my output directory is blank!. Obviously, something was wrong with the GTF file I supply for -M option.
How do I generate a suitable file for -M option?