Question about gffcompare using multiple reference annotations from different databases
Dear all,
I'm using 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.
After the 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 mitranscriptome and lncipedia gtfs and get the output which are not overlapped with these two gtfs using gffcompare.
Is it possible to do with gffcompare? How should I give the command for this?
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I would suggest you first try the GffCompare's manual.