Use string merge to merge full-length transcript GTF file

[Tang-pro]

Hi @gpertea @smoe

I used the above command to merge two GTF files, which were constructed by PacBio to represent full-length isoforms

stringtie --merge -G Ref_gene.gtf -o Gb.gtf final.gtf ML.filtered.gtf

cat final.gtf | cut -f3 | sort | uniq -c 1271660 CDS 1894956 exon 229526 transcript

cat ML.filtered.gtf | cut -f3 | sort | uniq -c 164895 CDS 179618 exon 28314 transcript

cat Gb.gtf | cut -f3 | sort | uniq -c 1298693 exon 183767 transcript

Why are there so many fewer transcripts after the merge?