I am trying to annotate my genome assembly using Maker. I have thousands of contigs, i discovered that few contigs failed during annotation. Since I can't begin a fresh annotation, I selected all the contigs that failed and ran maker on them.
now i want to merge off using gff3_merge
gff3_merge -d /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/muc1_genome_snap2.maker.output/muc1_genome_snap2_master_datastore_index.log /Users/emmannaemeka/Desktop/Gpm/maker/data/mucuna/Muc_unfi/sample_1.maker.output/sample_1_master_datastore_index.log gff3_merge -o genome_sample.all.gff
I have two log files 1. muc1_genome_snap2_master_datastore_index.log This is the log file from the first run that had failed contigs 2. sample_1_master_datastore_index.log This is the log file of the sequences in the first run that failed
How can i merge the Gffs to have one functional GFF for maker annotation?