convert~gff3_to_gtf

convert from gff3 to gtf

input_1:reference gene model file (gff3)

input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3

##gff-version   3
Bomo_Chr1	.	gene	20596	24779	0.13	+	.	ID=KWMTBOMO00001;Name=KWMTBOMO00001;Note=PREDICTED:_uncharacterized_protein_LOC106648510_[Trichogramma_pretiosum]
Bomo_Chr1	.	mRNA	20596	24779	0.13	+	.	ID=KWMTBOMO00001.mrna1;Name=KWMTBOMO00001;Parent=KWMTBOMO00001
Bomo_Chr1	.	transcription_start_site	20596	20596	.	+	.	Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	exon	20596	21325	.	+	.	ID=KWMTBOMO00001.mrna1.exon1;Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	start_codon	20692	20694	.	+	0	Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	CDS	20692	21325	0.44	+	0	ID=KWMTBOMO00001.mrna1.CDS1;Parent=KWMTBOMO00001.mrna1
Bomo_Chr1	.	initial	20692	21325	0.44	+	0	Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	intron	21326	21564	0.22	+	.	Parent=KWMTBOMO00001.mrna1;
Bomo_Chr1	.	CDS	21565	24719	0.31	+	2	ID=KWMTBOMO00001.mrna1.CDS2;Parent=KWMTBOMO00001.mrna1

Option

-c "8" -m "64"

Output

input_1/Bomo_gene_models.withnote.plus.NC_002355.withname.gtf

NC_002355.1	stdin	transcript	15095	15883	.	+	.	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; gene_name "COX3";
NC_002355.1	stdin	exon	15095	15883	.	+	.	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "COX3";
NC_002355.1	stdin	CDS	15095	15880	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "COX3";
NC_002355.1	stdin	start_codon	15095	15097	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "COX3";
NC_002355.1	stdin	stop_codon	15881	15883	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "COX3";
NC_002355.1	stdin	transcript	14403	15080	.	+	.	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; gene_name "ATP6";
NC_002355.1	stdin	exon	14403	15080	.	+	.	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "ATP6";
NC_002355.1	stdin	CDS	14403	15077	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "ATP6";
NC_002355.1	stdin	start_codon	14403	14405	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "ATP6";
NC_002355.1	stdin	stop_codon	15078	15080	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "ATP6";

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