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agshumate / Liftoff

An accurate GFF3/GTF lift over pipeline
GNU General Public License v3.0
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Liftoff for non-coding genes? #143

Open zmz1988 opened 1 year ago

zmz1988 commented 1 year ago

Hi, thanks for the nice tool! I really enjoy using it. I just have a question about lifting over the non-coding genes.

I'm using liftoff for a model species, and I lifted over the annotation from the reference to my own assembly (the same line/accession as the reference). I found that all the coding genes annotation were transferred well, but I missed all the non-coding genes in the new annotation, e.g. miRNA, lncRNA, rRNA...

So may I confirm with you that liftoff can not transfer the annotation of non-coding genes? If not, could you suggest me where I might do wrong?

My code is as below: liftoff -g ../reference.gff3 -o sample_liftoff.gff3 -u sample_unmapped_features.txt -p 10 -chroms match_chrom.txt -copies -polish sample.fasta reference.fasta

Thanks a lot for your help!

fpichon commented 1 year ago

Hello everybody. Same comment here! Thanks a lot for this very nice and useful tool! A great new feature would be to have non coding genes too!! Best,

EDIT: I finally could obtain non-coding genes using -f option. Just extract features from your GFF3 reference file: grep -v '#' my_reference.gff3 | cut -f3 | sort | uniq > features.txt Then use it with -f option: liftoff -g my_reference.gff3 -o my_outfile.gtf -f features.txt my_assembly.fasta my_reference.fa Hope it will help!