I'm trying to use TransDecoder to identify transcripts with high coding potential. In the previous step, I obtained several files with extensions .tmap, .tracking, .stats, .combined.gtf, and .refmap from cuffcompare results. I used the combined.gtf file obtained by filtering from these files as input for TransDecoder, but it resulted in an empty output file. On the TransDecoder Github account, they have provided sample code and files specifically for cufflinks. Initially, the .gtf file I obtained already had different columns compared to cufflinks. I suspected that this was due to using cuffcompare. The columns in the sample .gtf file are present in my .tmap file. In this situation, what steps should I follow? Thank you
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