GFF File Lift Over

If one has a GFF file associated with input contigs, one can lift them over to new RaGOO pseudomolecules.

Without Chimeric Contig Correction

# Get the data
cd /path/to/current/working/directory
ln -s /path/to/contigs.fasta
ln -s /path/to/reference.fasta
ln -s /path/to/genes.gff

# Run RaGOO
ragoo.py -g 100 contigs.fasta reference.fasta

# Get additional info
ls ragoo_output/orderings/* > orderings.fofn
samtools faidx contigs.fasta

# Lift-over
lift_over.py -g 100 genes.gff orderings.fofn contigs.fasta.fai > genes.ragoo.gff

Please note that the -g flag for both ragoo.py and lift_over.py must match. 100 is the default, and therefore unnecessary in my example, but it is there to highlight this point.

With Chimeric Contig Correction

# Get the data
cd /path/to/current/working/directory
ln -s /path/to/contigs.fasta
ln -s /path/to/reference.fasta
ln -s /path/to/genes.gff

# Run RaGOO
ragoo.py -b -gff genes.gff -g 100 contigs.fasta reference.fasta

# Get additional info
ls ragoo_output/orderings/* > orderings.fofn
samtools faidx ragoo_output/chimera_break/contigs.intra.chimera.broken.fa 

# Lift-over
lift_over.py -g 100 ragoo_output/chimera_break/genes.intra.chimera_broken.gff orderings.fofn ragoo_output/chimera_break/contigs.intra.chimera.broken.fa.fai > genes.ragoo.gff

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