feat: add functional tracks pipeline notebook

notebooks_pipelines/NTv3_650M_pos_hg38_chr19_6700000_6831072.gff3

@@ -1,107 +0,0 @@
-##gff-version 3
-# model: InstaDeepAI/NTv3_650M_pos
-# window: chr19:6700000-6831072 (hg38); predictions on central 37.5%: chr19:6740960-6790112
-chr19	NTv3_HMM	intron	6740961	6740995	0.975	.	.	ID=INTRON_1;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	start_codon	6740996	6741013	0.355	.	.	ID=START_CODON_2;Name=START_CODON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,191,255
-chr19	NTv3_HMM	exon	6741014	6741124	0.673	.	.	ID=EXON_3;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6741125	6741125	0.857	.	.	ID=SPLICE_DONOR_4;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6741126	6741224	0.974	.	.	ID=INTRON_5;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6741225	6741225	0.930	.	.	ID=SPLICE_ACCEPTOR_6;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6741226	6741280	0.693	.	.	ID=EXON_7;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6741281	6741281	0.837	.	.	ID=SPLICE_DONOR_8;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6741282	6742966	0.959	.	.	ID=INTRON_9;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6742967	6742967	0.958	.	.	ID=SPLICE_ACCEPTOR_10;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6742968	6743113	0.841	.	.	ID=EXON_11;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6743114	6743114	0.779	.	.	ID=SPLICE_DONOR_12;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6743115	6743193	0.963	.	.	ID=INTRON_13;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6743194	6743194	0.910	.	.	ID=SPLICE_ACCEPTOR_14;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6743195	6743255	0.845	.	.	ID=EXON_15;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6743256	6743256	0.782	.	.	ID=SPLICE_DONOR_16;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6743257	6743493	0.970	.	.	ID=INTRON_17;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6743494	6743494	0.780	.	.	ID=SPLICE_ACCEPTOR_18;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6743495	6743597	0.876	.	.	ID=EXON_19;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6743598	6743598	0.856	.	.	ID=SPLICE_DONOR_20;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6743599	6743707	0.951	.	.	ID=INTRON_21;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6743708	6743708	0.856	.	.	ID=SPLICE_ACCEPTOR_22;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6743709	6743835	0.812	.	.	ID=EXON_23;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6743836	6743836	0.887	.	.	ID=SPLICE_DONOR_24;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6743837	6744553	0.989	.	.	ID=INTRON_25;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6744554	6744554	0.972	.	.	ID=SPLICE_ACCEPTOR_26;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6744555	6744700	0.977	.	.	ID=EXON_27;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	intron	6744701	6744799	0.972	.	.	ID=INTRON_28;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6744800	6744800	0.954	.	.	ID=SPLICE_ACCEPTOR_29;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6744801	6744993	0.977	.	.	ID=EXON_30;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6744994	6744994	0.886	.	.	ID=SPLICE_DONOR_31;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6744995	6746451	0.979	.	.	ID=INTRON_32;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6746452	6746452	0.938	.	.	ID=SPLICE_ACCEPTOR_33;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6746453	6746560	0.840	.	.	ID=EXON_34;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6746561	6746561	0.947	.	.	ID=SPLICE_DONOR_35;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6746562	6749933	0.973	.	.	ID=INTRON_36;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6749934	6749934	0.693	.	.	ID=SPLICE_ACCEPTOR_37;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6749935	6750065	0.918	.	.	ID=EXON_38;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6750066	6750066	0.783	.	.	ID=SPLICE_DONOR_39;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6750067	6750291	0.955	.	.	ID=INTRON_40;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6750292	6750292	0.960	.	.	ID=SPLICE_ACCEPTOR_41;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6750293	6750430	0.959	.	.	ID=EXON_42;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6750431	6750431	0.723	.	.	ID=SPLICE_DONOR_43;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6750432	6750511	0.939	.	.	ID=INTRON_44;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6750512	6750512	0.750	.	.	ID=SPLICE_ACCEPTOR_45;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6750513	6750632	0.902	.	.	ID=EXON_46;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6750633	6750633	0.917	.	.	ID=SPLICE_DONOR_47;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6750634	6751062	0.961	.	.	ID=INTRON_48;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_acceptor_site	6751063	6751063	0.694	.	.	ID=SPLICE_ACCEPTOR_49;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6751064	6751199	0.558	.	.	ID=EXON_50;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	stop_codon	6751200	6751212	0.332	.	.	ID=STOP_CODON_51;Name=STOP_CODON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=220,20,60
-chr19	NTv3_HMM	three_prime_UTR	6751213	6751488	0.965	+	.	ID=UTR3_PLUS_52;Name=UTR3_PLUS;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=34,139,34
-chr19	NTv3_HMM	polyA_signal	6751489	6751507	0.355	.	.	ID=POLYA_SIGNAL_53;Name=POLYA_SIGNAL;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=139,69,19
-chr19	NTv3_HMM	start_codon	6751508	6752169	0.002	.	.	ID=START_CODON_54;Name=START_CODON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,191,255
-chr19	NTv3_HMM	polyA_signal	6752170	6752187	0.432	.	.	ID=POLYA_SIGNAL_55;Name=POLYA_SIGNAL;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=139,69,19
-chr19	NTv3_HMM	three_prime_UTR	6752188	6752571	0.839	-	.	ID=UTR3_MINUS_56;Name=UTR3_MINUS;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=34,139,34
-chr19	NTv3_HMM	stop_codon	6752572	6752752	0.136	.	.	ID=STOP_CODON_57;Name=STOP_CODON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=220,20,60
-chr19	NTv3_HMM	splice_acceptor_site	6752753	6752753	0.798	.	.	ID=SPLICE_ACCEPTOR_58;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6752754	6753455	0.910	.	.	ID=INTRON_59;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_donor_site	6753456	6753456	0.766	.	.	ID=SPLICE_DONOR_60;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6753457	6753640	0.953	.	.	ID=EXON_61;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_acceptor_site	6753641	6753641	0.939	.	.	ID=SPLICE_ACCEPTOR_62;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6753642	6754051	0.985	.	.	ID=INTRON_63;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_donor_site	6754052	6754052	0.844	.	.	ID=SPLICE_DONOR_64;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6754053	6754161	0.908	.	.	ID=EXON_65;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_acceptor_site	6754162	6754163	0.633	.	.	ID=SPLICE_ACCEPTOR_66;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6754164	6754250	0.962	.	.	ID=INTRON_67;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_donor_site	6754251	6754251	0.875	.	.	ID=SPLICE_DONOR_68;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6754252	6754424	0.965	.	.	ID=EXON_69;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_acceptor_site	6754425	6754425	0.791	.	.	ID=SPLICE_ACCEPTOR_70;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6754426	6754615	0.975	.	.	ID=INTRON_71;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_donor_site	6754616	6754616	0.953	.	.	ID=SPLICE_DONOR_72;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6754617	6754730	0.731	.	.	ID=EXON_73;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_acceptor_site	6754731	6754731	0.822	.	.	ID=SPLICE_ACCEPTOR_74;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6754732	6754830	0.975	.	.	ID=INTRON_75;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_donor_site	6754831	6754831	0.944	.	.	ID=SPLICE_DONOR_76;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6754832	6755314	0.757	.	.	ID=EXON_77;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_acceptor_site	6755315	6755315	0.713	.	.	ID=SPLICE_ACCEPTOR_78;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6755316	6759593	0.988	.	.	ID=INTRON_79;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_donor_site	6759594	6759594	0.928	.	.	ID=SPLICE_DONOR_80;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6759595	6759669	0.840	.	.	ID=EXON_81;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_acceptor_site	6759670	6759670	0.901	.	.	ID=SPLICE_ACCEPTOR_82;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6759671	6760637	0.985	.	.	ID=INTRON_83;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_donor_site	6760638	6760638	0.928	.	.	ID=SPLICE_DONOR_84;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6760639	6760985	0.748	.	.	ID=EXON_85;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_acceptor_site	6760986	6760987	0.603	.	.	ID=SPLICE_ACCEPTOR_86;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6760988	6763679	0.984	.	.	ID=INTRON_87;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_donor_site	6763680	6763680	0.759	.	.	ID=SPLICE_DONOR_88;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	exon	6763681	6763732	0.663	.	.	ID=EXON_89;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	five_prime_UTR	6763733	6763815	0.840	-	.	ID=UTR5_MINUS_90;Name=UTR5_MINUS;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,128,0
-chr19	NTv3_HMM	splice_acceptor_site	6763816	6763816	0.869	.	.	ID=SPLICE_ACCEPTOR_91;Name=SPLICE_ACCEPTOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6763817	6767386	0.976	.	.	ID=INTRON_92;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072
-chr19	NTv3_HMM	splice_donor_site	6767387	6767387	0.902	.	.	ID=SPLICE_DONOR_93;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	start_codon	6767388	6767411	0.051	.	.	ID=START_CODON_94;Name=START_CODON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,191,255
-chr19	NTv3_HMM	five_prime_UTR	6767412	6767514	0.578	-	.	ID=UTR5_MINUS_95;Name=UTR5_MINUS;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,128,0
-chr19	NTv3_HMM	start_codon	6767515	6769347	0.009	.	.	ID=START_CODON_96;Name=START_CODON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,191,255
-chr19	NTv3_HMM	TF_binding_site	6769348	6769521	0.506	.	.	ID=CTCF_97;Name=CTCF;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=148,0,211
-chr19	NTv3_HMM	start_codon	6769522	6772696	0.002	.	.	ID=START_CODON_98;Name=START_CODON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,191,255
-chr19	NTv3_HMM	five_prime_UTR	6772697	6772806	0.885	+	.	ID=UTR5_PLUS_99;Name=UTR5_PLUS;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,128,0
-chr19	NTv3_HMM	start_codon	6772807	6772810	0.694	.	.	ID=START_CODON_100;Name=START_CODON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,191,255
-chr19	NTv3_HMM	five_prime_UTR	6772811	6772922	0.748	+	.	ID=UTR5_PLUS_101;Name=UTR5_PLUS;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,128,0
-chr19	NTv3_HMM	exon	6772923	6773010	0.635	.	.	ID=EXON_102;Name=EXON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,255
-chr19	NTv3_HMM	splice_donor_site	6773011	6773011	0.884	.	.	ID=SPLICE_DONOR_103;Name=SPLICE_DONOR;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072;color=0,0,0
-chr19	NTv3_HMM	intron	6773012	6790112	0.972	.	.	ID=INTRON_104;Name=INTRON;model=InstaDeepAI/NTv3_650M_pos;assembly=hg38;window=chr19:6700000-6831072

notebooks_pipelines/bigwig_outputs/HepG2_CTCF.bw

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tabs/annotation.html

@@ -2,8 +2,13 @@
   <h2>🧬 NTv3 Post-Trained Genome Annotation</h2>
   <p>This notebook demonstrates how to use the NTv3 post-trained model to perform genome annotation directly from a DNA sequence. It relies on a pipeline that applies a Hidden Markov Model (HMM) to the per-base probabilities returned by NTv3, converting them into a coherent gene model that respects biological constraints and valid transitions between genomic elements.</p>
   <p>The pipeline abstracts away all the underlying steps: running inference with the model, retrieving and processing the predicted probabilities, and applying the HMM to generate a consistent annotation. It returns a ready-to-use GFF file that can be visualized in any genome browser for the sequence of interest.</p>
-  <p>If you're interested in exploring the intermediate probabilities, please refer to the <a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks/01_tracks_prediction.ipynb" target="_blank" rel="noopener">track-prediction notebook</a>. These probabilities can be useful for assessing model confidence and identifying potentially interesting biological regions. This notebook focuses on the higher-level task of producing gene annotations directly from raw DNA.</p>
+  <p>If you're interested in exploring the intermediate probabilities, please refer to the <a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_tutorials/01_tracks_prediction.ipynb" target="_blank" rel="noopener">track-prediction notebook</a>. These probabilities can be useful for assessing model confidence and identifying potentially interesting biological regions. This notebook focuses on the higher-level task of producing gene annotations directly from raw DNA.</p>
   <p><strong>📝 Note for Google Colab users:</strong> This notebook is compatible with Colab! For faster inference, make sure to enable GPU: Runtime → Change runtime type → GPU (T4 or better recommended).</p>
+  <p>
+    <strong>🔗 Quick links:</strong><br>
+    • <a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_pipelines/02_genome_annotation.ipynb" target="_blank" rel="noopener">View notebook on Hugging Face</a> (includes "Open in Colab" button)<br>
+    • <a href="https://colab.research.google.com/github/InstaDeepAI/ntv3/blob/main/notebooks_pipelines/02_genome_annotation.ipynb" target="_blank" rel="noopener">Open directly in Google Colab</a>
+  </p>
 </div>
 
 <div class="grid">
@@ -41,11 +46,11 @@ print(f"Original sequence length: {len(seq)}")
 # Crop to multiple of 128 (the pipeline will crop again, but this is a no-op once divisible)
 seq = seq[:int(len(seq) // 128) * 128]
 print(f"Cropped sequence length: {len(seq)}, {len(seq) / 128} transformer tokens")</code></pre></div>
-    <p style="margin-top: 15px; color: var(--muted); font-size: 13px;">
-      <strong>Example output:</strong><br>
+    <div style="margin-top: 15px; padding: 12px 16px; background: rgba(0, 0, 0, 0.4); border: 1px solid var(--border); border-radius: 8px; font-family: var(--mono); font-size: 12px; color: rgba(255, 255, 255, 0.85); line-height: 1.6;">
+      <strong style="color: var(--muted);">Output:</strong><br>
       Original sequence length: 131072<br>
       Cropped sequence length: 131072, 1024.0 transformer tokens
-    </p>
+    </div>
   </div>
 
   <div class="card" style="grid-column: span 12;">
@@ -72,6 +77,14 @@ start_time = time.time()
 gff_text = ntv3_gff(inputs)
 end_time = time.time()
 print(f"Inference + decoding time: {end_time - start_time:.2f} seconds")</code></pre></div>
+    <div style="margin-top: 15px; padding: 12px 16px; background: rgba(0, 0, 0, 0.4); border: 1px solid var(--border); border-radius: 8px; font-family: var(--mono); font-size: 12px; color: rgba(255, 255, 255, 0.85); line-height: 1.6;">
+      <strong style="color: var(--muted);">Output:</strong><br>
+      A new version of the following files was downloaded from https://huggingface.co/InstaDeepAI/NTv3_650M_pos:<br>
+      - ntv3_gff_pipeline.py<br>
+      . Make sure to double-check they do not contain any added malicious code. To avoid downloading new versions of the code file, you can pin a revision.<br>
+      Device set to use cpu<br>
+      Inference + decoding time: 53.09 seconds
+    </div>
     <p style="margin-top: 15px; color: var(--muted); font-size: 13px;">
       The pipeline performs all the necessary steps: running inference with the model, retrieving and processing the predicted probabilities, and applying the HMM to generate a consistent annotation.
     </p>
@@ -88,9 +101,10 @@ with open(output_filename, "w") as output_file:
     output_file.write(gff_text)
 
 print(f"Saved GFF file to {output_filename}")</code></pre></div>
-    <p style="margin-top: 15px; color: var(--muted); font-size: 13px;">
-      <strong>Example output:</strong> Saved GFF file to NTv3_650M_pos_hg38_chr19_6700000_6831072.gff3
-    </p>
+    <div style="margin-top: 15px; padding: 12px 16px; background: rgba(0, 0, 0, 0.4); border: 1px solid var(--border); border-radius: 8px; font-family: var(--mono); font-size: 12px; color: rgba(255, 255, 255, 0.85); line-height: 1.6;">
+      <strong style="color: var(--muted);">Output:</strong><br>
+      Saved GFF file to NTv3_650M_pos_hg38_chr19_6700000_6831072.gff3
+    </div>
   </div>
 
   <div class="card" style="grid-column: span 12;">

tabs/functional_tracks.html

@@ -4,6 +4,11 @@
   <p>The pipeline abstracts away all the underlying steps: running inference with the model and plotting the predictions per tracks.</p>
   <p>If you're interested in exploring the intermediate probabilities, please refer to the <a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_tutorials/01_tracks_prediction.ipynb" target="_blank" rel="noopener">track-prediction notebook</a>.</p>
   <p><strong>📝 Note for Google Colab users:</strong> This notebook is compatible with Colab! For faster inference, make sure to enable GPU: Runtime → Change runtime type → GPU (T4 or better recommended).</p>
+  <p>
+    <strong>🔗 Quick links:</strong><br>
+    • <a href="https://huggingface.co/spaces/InstaDeepAI/ntv3/blob/main/notebooks_pipelines/01_functional_track_prediction.ipynb" target="_blank" rel="noopener">View notebook on Hugging Face</a> (includes "Open in Colab" button)<br>
+    • <a href="https://colab.research.google.com/github/InstaDeepAI/ntv3/blob/main/notebooks_pipelines/01_functional_track_prediction.ipynb" target="_blank" rel="noopener">Open directly in Google Colab</a>
+  </p>
 </div>
 
 <div class="grid">
@@ -47,11 +52,11 @@ print(f"Original sequence length: {len(seq)}")
 # Crop to multiple of 128 (the pipeline will crop again, but this is a no-op once divisible)
 seq = seq[:int(len(seq) // 128) * 128]
 print(f"Cropped sequence length: {len(seq)}, {len(seq) / 128} transformer tokens")</code></pre></div>
-    <p style="margin-top: 15px; color: var(--muted); font-size: 13px;">
-      <strong>Example output:</strong><br>
+    <div style="margin-top: 15px; padding: 12px 16px; background: rgba(0, 0, 0, 0.4); border: 1px solid var(--border); border-radius: 8px; font-family: var(--mono); font-size: 12px; color: rgba(255, 255, 255, 0.85); line-height: 1.6;">
+      <strong style="color: var(--muted);">Output:</strong><br>
       Original sequence length: 131072<br>
       Cropped sequence length: 131072, 1024.0 transformer tokens
-    </p>
+    </div>
   </div>
 
   <div class="card" style="grid-column: span 12;">
@@ -90,6 +95,15 @@ ntv3_predictions = ntv3_tracks(
 end_time = time.time()
 
 print(f"Inference + decoding time: {end_time - start_time:.2f} seconds")</code></pre></div>
+    <div style="margin-top: 15px; padding: 12px 16px; background: rgba(0, 0, 0, 0.4); border: 1px solid var(--border); border-radius: 8px; font-family: var(--mono); font-size: 12px; color: rgba(255, 255, 255, 0.85); line-height: 1.6;">
+      <strong style="color: var(--muted);">Output:</strong><br>
+      Device set to use cpu<br>
+      Running on device: cpu<br>
+      Inference + decoding time: 38.32 seconds
+    </div>
+    <div style="margin-top: 20px;">
+      <img src="assets/output_tracks.png" alt="Output tracks plot" style="width: 100%; height: auto; border-radius: 12px; border: 1px solid var(--border);" />
+    </div>
     <p style="margin-top: 15px; color: var(--muted); font-size: 13px;">
       The pipeline performs all the necessary steps: running inference with the model and plotting the predictions for the specified tracks and genomic elements.
     </p>
@@ -166,7 +180,27 @@ for i, (display_name, track_id, track_idx) in enumerate(track_data_list):
     
     print(f"  Saved {i + 1}/{len(track_data_list)}: {display_name} ({track_clean_name}.bw)")
 
-print(f"\n✅ Successfully saved {len(track_data_list)} BigWig files to '{output_dir}/'")</code></pre></div>
+print(f"\n✅ Successfully saved {len(track_data_list)} BigWig files to '{output_dir}/'")
+print(f"   Files: {', '.join([name.replace(' ', '_').replace('/', '_').replace('-', '_') for name, _, _ in track_data_list])}")</code></pre></div>
+    <div style="margin-top: 15px; padding: 12px 16px; background: rgba(0, 0, 0, 0.4); border: 1px solid var(--border); border-radius: 8px; font-family: var(--mono); font-size: 12px; color: rgba(255, 255, 255, 0.85); line-height: 1.6; white-space: pre-wrap;">
+      <strong style="color: var(--muted);">Output:</strong><br>Found 8 tracks to save from tracks_to_plot
+Input region: chr19:6700000-6831072 (length: 131,072 bp)
+Prediction region: chr19:6740960-6790112 (length: 49,152 bp)
+Number of positions: 49152
+
+Saving BigWig files to 'bigwig_outputs/' directory...
+  Saved 1/8: K562 RNA-seq (K562_RNA_seq.bw)
+  Saved 2/8: K562 DNAse (K562_DNAse.bw)
+  Saved 3/8: K562 H3k4me3 (K562_H3k4me3.bw)
+  Saved 4/8: K562 CTCF (K562_CTCF.bw)
+  Saved 5/8: HepG2 RNA-seq (HepG2_RNA_seq.bw)
+  Saved 6/8: HepG2 DNAse (HepG2_DNAse.bw)
+  Saved 7/8: HepG2 H3k4me3 (HepG2_H3k4me3.bw)
+  Saved 8/8: HepG2 CTCF (HepG2_CTCF.bw)
+
+✅ Successfully saved 8 BigWig files to 'bigwig_outputs/'
+   Files: K562_RNA_seq, K562_DNAse, K562_H3k4me3, K562_CTCF, HepG2_RNA_seq, HepG2_DNAse, HepG2_H3k4me3, HepG2_CTCF
+    </div>
     <p style="margin-top: 15px; color: var(--muted); font-size: 13px;">
       This saves each selected functional track as a separate BigWig file that can be visualized in genome browsers. The files are saved with user-friendly display names (e.g., "K562_RNA_seq.bw").
     </p>