HISAT2 for alignment and
Stringtie for assembling transcripts for each sample and then I used
stringtie --merge to merge the transcripts from all samples. In the
Stringtie step I used
gencode.v19.annotation.gtf file as reference annotation.
stringtie --merge I'm interested to use
gffcompare to compare the transcripts I got with other reference annotation files from different databases.
I would like to use
lncipedia gtfs and get the output which are not overlapped with these two gtfs using
Is it possible to do with
gffcompare? How should I give the command for this?