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Liftoff feature mapping

Using Liftoff for gene annotation and I noticed that many of the features do not get lifted over in the final .gff . I see that the gene hierarchy features appear mostly preserved (gene, exon, mRNA, transcripts, CDS), but missing metadata related features (match, cDNA_match), and other genetic features (intron, pseudogene, region, miRNA).

This is my first time using Liftoff, and I just wanted to make sure that this was expected behavior. The explanation I have come up with so far is that Liftoff is focused on lifting over 'gene model' features that are hierarchically related which is why 'match' and 'cDNA_match' wouldn't be in the result and high quality alignments (which is why pseudogene features are absent).

Anyone to confirm/deny or offer any expertise?

Thank you

annotation liftoff
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updated by lauraashaley • lauraashaley • written by Christopher • Christopher

yep, your hunch is correct: liftoff focuses on transferring the actual gene models by default.

I seem to remember there might be a parameter to change , or at least specify, other features to be transferred though

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written by lieven.sterck lieven.sterck

Looks like that parameter is -f. From the liftoff manual:

Feature Types By default, 'gene' features and all child features of genes (i.e. trancripts, mRNA, exons, CDS, UTRs) will be lifted over. The -f parameter can be used to specify a file containing a list of additional parent feature types you wish to lift-over. Note: feature IDs must be unique for every feature and may not contain spaces. Example of a feature types file would be the following:

biological_region
miRNA
repeat_element
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written by GenoMax GenoMax

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