Hello, I'm currently conducting RNA-seq analysis and using cuffcompare to distinguish mRNA and known lncRNA within my samples. I have a question.

1) I performed cuffcompare on my sample's GTF list, using an mRNA.gtf file as the annotation, and identified transcripts with class code "=" as mRNA, which I then separated. Below is my command:

cuffcompare merged.gtf -r ../Annotation/gencode.v29lift37.coding_RNAs.gtf -s ../WholeGenomeFasta/genome.fa -o cuffcmp

2) After removing mRNA from the combined.gtf file,(and this new file name is noncoding.gtf) I ran cuffcompare again, this time using lncRNA.gtf from Gencode as the annotation. Below is my command:

cuffcompare noncoding.gtf -r ../Annotation/gencode.v29lift37.long_noncoding_RNAs.gtf -s ../WholeGenomeFasta/genome.fa -o cmptoknown

I expected that transcripts matching the known lncRNAs in the annotation would be labeled with the class code "=", which would allow me to easily extract the known lncRNAs. However, after running cuffcompare for the second time, I found that no trasncritps were labeled with the "=" class code. Below is my result:

Given that there should be transcripts overlapping with the long noncoding RNA annoation file, why does it seem that none of them are identified?