I am using a piece of software (PARalyzer for PAR-clip data). The pipeline I am using requires a GENCODE format .gtf annotation. Since the official GENCODE rat annotation is not available, maybe somebody tried re-structuring the UCSC annotation to fit the GENCODE format ?
I already tried appending a second "filler" column to match the column order, but there are way more differences in the last multi-entry column. The home-made annotation with filler column didn't work (all works perfectly for GENCODE human and mouse annotation).
I would be very thankful for any tips or maybe files ;)
Have a nice weekend!