3. Tutorial¶

3.1. Prepare your prerequisites¶

install dependencies
prepare outputs from previous MAKER run
run detect_fused_gene.py
run extract_to_maker.py
review results or trouble shooting

3.2. Example - rice chromosome 9¶

detect fused gene candidates:

python bin/1_detect_fused_gene.py -i resources/rice_chr9_transcript.fa -g resources/rice_chr9.gff -n 30 -p chr9_S1R1

split fused gene and locally re-annotation:

python bin/2_extract_to_maker.py -i resources/rice_chr9.fa -d chr9_S1R1/gff.db -c chr9_S1R1/break_coordinates.brk \
-t resources/rice_chr9_ctl/ -n 28 -p chr9_S2R1

drop fused gene entries from original transcript and protein sequence fasta files:

mkdir chr9_post_process

python bin/3_process_fasta_file.py -i resources/rice_chr9_transcript.fa -g chr9_S2R1/gene_features_wo_fused.gff  \
-o chr9_post_process/rice_chr9_transcript_drop_fused.fa

python bin/3_process_fasta_file.py -i resources/rice_chr9_protein.fa -g chr9_S2R1/gene_features_wo_fused.gff  \
-o chr9_post_process/rice_chr9_protein_drop_fused.fa

run maker standard on defused gene set. MAKER standard is a procedure to get rid of low-quality gene models:

python bin/4_run_maker_standard.py -t chr9_S2R1/merged_defused_transcripts.fa -p chr9_S2R1/merged_defused_protein.fa \
-g chr9_S2R1/merged_defused.all.mod.gff -a Pfam/Pfam-A.hmm -o chr9_post_process/

generate AED score improvement plot:

python bin/5_generate_report.py -b chr9_S1R1/break_coordinates.brk \
-i resources/rice_chr9.gff \
-g chr9_post_process/merged_defused.all.mod.std.gff \
-o chr9_post_process/chr9

final assembly:

mv chr9_S2R1/gene_features_wo_fused.gff chr9_post_process/

cd chr9_post_process

cat gene_features_wo_fused.gff merged_defused.all.mod.std.gff > chr9_V1.gff
cat rice_chr9_transcript_drop_fused.fa merged_defused_transcripts.std.fa > chr9_V1_transcripts.fa
cat rice_chr9_protein_drop_fused.fa merged_defused_protein.std.fa > chr9_V1_protein.fa

DONE Final outputs:

chr9_V1.gff
chr9_V1_transcripts.fa
chr9_V1_protein.fa