A particularly small number were identified, wanting to remove transposon genes in gff3 after evm integration

[wencyuan]

(TEsorter) wcyuan@n03:/data/fuzhiyuan/evm/tesorter/p4$ ln -s /home/wcyuan/data/fuzhiyuan/evm/p4/P4_clean_EVM.gff3
gffread P4_clean_EVM.gff3 -g /home/wcyuan/data/fuzhiyuan/p4/P4_genome.masked.fa -x p4_gene_cds.fa
TEsorter p4_gene_cds.fa -db rexdb-plant -eval 1e-6 -p 20 -pre p4
(TEsorter) wcyuan@fat1:/data/fuzhiyuan/evm/tesorter/p4$ grep -v "^#" p4.cls.tsv | cut -f1 | sort | uniq > p4_TE-genes.txt
cat p4_TE-genes.txt |wc -l
1135

[zhangrengang]

gff3 output from GENOME mode can be directly input to EVM. An example:

ref=genome.fasta
TEsorter $ref -genome -p 32 -db rexdb -cov 30 -eval 1e-5 -prob 0.9 -score 1 > tesorter.stats

# EVM
partition_EVM_inputs.pl --genome $ref --gene_predictions PRED_GFF3 --transcript_alignments TRANS_GFF3 \
        --protein_alignments PRO_GFF3 --repeats $ref.rexdb.dom.gff3 \
        --segmentSize 1000000 --overlapSize 100000 --partition_listing partitions_list.out
......