Added Yang analysis

naobservatory · Mar 16, 2024 · eab310b · eab310b
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commit eab310b
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Showing 46 changed files with 96,424 additions and 18 deletions.
diff --git a/data/2024-02-23_rothman-1/rothman-putative-viral.fasta b/data/2024-02-23_rothman-1/rothman-putative-viral.fasta
diff --git a/data/2024-02-23_rothman-1/rothman-unclear-viral.fasta b/data/2024-02-23_rothman-1/rothman-unclear-viral.fasta
diff --git a/data/2024-03-15_yang/bracken_counts.tsv b/data/2024-03-15_yang/bracken_counts.tsv
@@ -0,0 +1,29 @@
+name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads	sample
+Viruses	10239	D	1177416	94	1177510	0.71603000000000006	SRR12204848
+Bacteria	2	D	450804	607	451411	0.2745	SRR12204848
+Eukaryota	2759	D	14313	104	14417	0.00877	SRR12204848
+Archaea	2157	D	1155	0	1155	7e-4	SRR12204848
+Viruses	10239	D	7304199	760	7304959	0.97407	SRR12204851
+Bacteria	2	D	128185	155	128340	0.01711	SRR12204851
+Eukaryota	2759	D	65495	398	65893	0.00879	SRR12204851
+Archaea	2157	D	209	0	209	3e-5	SRR12204851
+Viruses	10239	D	8227744	262	8228006	0.96664	SRR12204735
+Bacteria	2	D	266855	563	267418	0.03142	SRR12204735
+Eukaryota	2759	D	15523	214	15737	0.00185	SRR12204735
+Archaea	2157	D	815	0	815	1e-4	SRR12204735
+Viruses	10239	D	10299514	859	10300373	0.97579	SRR12204847
+Bacteria	2	D	183073	268	183341	0.01737	SRR12204847
+Eukaryota	2759	D	71651	249	71900	0.00681	SRR12204847
+Archaea	2157	D	348	0	348	3e-5	SRR12204847
+Viruses	10239	D	10191905	789	10192694	0.96897	SRR12204849
+Bacteria	2	D	283456	295	283751	0.02697	SRR12204849
+Eukaryota	2759	D	42072	235	42307	0.00402	SRR12204849
+Archaea	2157	D	371	0	371	4e-5	SRR12204849
+Viruses	10239	D	16212002	1266	16213268	0.9801	SRR12204850
+Bacteria	2	D	271416	250	271666	0.01642	SRR12204850
+Eukaryota	2759	D	57046	207	57253	0.00346	SRR12204850
+Archaea	2157	D	345	0	345	2e-5	SRR12204850
+Viruses	10239	D	20653117	2167	20655284	0.97498	SRR12204734
+Eukaryota	2759	D	399469	658	400127	0.01889	SRR12204734
+Bacteria	2	D	129556	155	129711	0.00612	SRR12204734
+Archaea	2157	D	173	0	173	1e-5	SRR12204734
diff --git a/data/2024-03-15_yang/hv_hits_putative_filtered.tsv.gz b/data/2024-03-15_yang/hv_hits_putative_filtered.tsv.gz
diff --git a/data/2024-03-15_yang/kraken/SRR12204734.report.gz b/data/2024-03-15_yang/kraken/SRR12204734.report.gz
diff --git a/data/2024-03-15_yang/kraken/SRR12204735.report.gz b/data/2024-03-15_yang/kraken/SRR12204735.report.gz
diff --git a/data/2024-03-15_yang/kraken/SRR12204847.report.gz b/data/2024-03-15_yang/kraken/SRR12204847.report.gz
diff --git a/data/2024-03-15_yang/kraken/SRR12204848.report.gz b/data/2024-03-15_yang/kraken/SRR12204848.report.gz
diff --git a/data/2024-03-15_yang/kraken/SRR12204849.report.gz b/data/2024-03-15_yang/kraken/SRR12204849.report.gz
diff --git a/data/2024-03-15_yang/kraken/SRR12204850.report.gz b/data/2024-03-15_yang/kraken/SRR12204850.report.gz
diff --git a/data/2024-03-15_yang/kraken/SRR12204851.report.gz b/data/2024-03-15_yang/kraken/SRR12204851.report.gz
diff --git a/data/2024-03-15_yang/qc_adapter_stats.tsv b/data/2024-03-15_yang/qc_adapter_stats.tsv
diff --git a/data/2024-03-15_yang/qc_basic_stats.tsv b/data/2024-03-15_yang/qc_basic_stats.tsv
@@ -0,0 +1,36 @@
+sample	percent_gc	mean_seq_len	n_read_pairs	percent_duplicates	n_bases_approx	per_base_sequence_quality	per_sequence_quality_scores	per_base_sequence_content	per_sequence_gc_content	per_base_n_content	sequence_length_distribution	sequence_duplication_levels	overrepresented_sequences	adapter_content	stage
+SRR12204734	39.5	150	201880938	90.7717377720592	60400000000	pass/pass	pass/pass	warn/warn	fail/fail	pass/pass	pass/pass	fail/fail	fail/fail	warn/warn	raw_concat
+SRR12204735	47	150	283160455	95.51551719676526	84800000000	pass/pass	pass/pass	fail/fail	fail/fail	pass/pass	pass/pass	fail/fail	fail/warn	fail/fail	raw_concat
+SRR12204847	45	150	231329232	92.56001460768748	69200000000	pass/pass	pass/pass	warn/warn	fail/fail	pass/pass	pass/pass	fail/fail	fail/fail	fail/fail	raw_concat
+SRR12204848	51	150	202643208	95.53873780345313	60600000000	pass/pass	pass/pass	fail/fail	fail/fail	pass/pass	pass/pass	fail/fail	fail/fail	fail/fail	raw_concat
+SRR12204849	35.5	151	161802900	88.85075222314512	48800000000	pass/pass	pass/pass	warn/warn	fail/fail	pass/pass	pass/pass	fail/fail	fail/fail	fail/warn	raw_concat
+SRR12204850	36	151	167982692	90.09373094713723	50600000000	pass/pass	pass/pass	warn/warn	fail/fail	pass/pass	pass/pass	fail/fail	fail/fail	fail/fail	raw_concat
+SRR12204851	43	150	170134059	92.62017424514895	51000000000	pass/pass	pass/pass	warn/fail	fail/fail	pass/pass	pass/pass	fail/fail	fail/fail	fail/fail	raw_concat
+SRR12204734	45	148.07460023939973	162424586	91.50496763433529	48000000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/warn	pass/pass	cleaned
+SRR12204735	48	134.8960562526966	267060975	96.41354839668256	72000000000	pass/pass	pass/pass	fail/fail	warn/fail	pass/pass	warn/warn	fail/fail	fail/warn	pass/pass	cleaned
+SRR12204847	46	142.65389383501235	194014679	95.87937996935213	55200000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	cleaned
+SRR12204848	53	133.40296443215414	188352059	96.62219715301714	50200000000	pass/pass	pass/pass	fail/fail	fail/fail	pass/pass	warn/warn	fail/fail	fail/fail	pass/pass	cleaned
+SRR12204849	46	147.12631696010084	113893067	87.60569617495524	33400000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	cleaned
+SRR12204850	46	147.81841879907358	123497107	89.58239283069446	36400000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	cleaned
+SRR12204851	45	135.5092357485163	142465605	94.58982055969736	38600000000	pass/pass	pass/pass	fail/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	cleaned
+SRR12204734	44	147.94660395077653	42524045	54.267402657941346	12500000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/warn	warn/pass	pass/pass	dedup
+SRR12204735	46	145.1408374419375	29215924	56.28787243047052	8400000000	pass/pass	pass/pass	fail/warn	pass/warn	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	dedup
+SRR12204847	45	146.018110968127	22760103	54.77427564702265	6600000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	dedup
+SRR12204848	50	143.5622973088183	15236541	53.989747908352626	4200000000	pass/pass	pass/pass	fail/warn	fail/pass	pass/pass	warn/warn	fail/fail	warn/warn	pass/pass	dedup
+SRR12204849	46.5	147.2150017043599	33801546	63.63418888433513	9800000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	dedup
+SRR12204850	46	147.46577813635417	35871483	72.71386975084044	10400000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	dedup
+SRR12204851	45	138.225483151466	15734455	49.46810554622455	4200000000	pass/pass	pass/pass	fail/warn	pass/pass	pass/pass	warn/warn	fail/warn	warn/pass	pass/pass	dedup
+SRR12204734	43.5	147.96998874438242	40855155	54.14043294301499	12000000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/warn	warn/pass	pass/pass	ribo_initial
+SRR12204735	45	145.73967113646307	24514241	53.991554259594025	7000000000	pass/pass	pass/pass	fail/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	ribo_initial
+SRR12204847	45	146.2460857721332	21049937	54.2252790089598	6000000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/warn	warn/pass	pass/pass	ribo_initial
+SRR12204848	49	143.33691508594347	10328184	47.60644892527266	2800000000	pass/pass	pass/pass	fail/warn	fail/pass	pass/pass	warn/warn	warn/warn	warn/warn	pass/pass	ribo_initial
+SRR12204849	46	147.22951840870846	31415186	63.1738693114621	9200000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	ribo_initial
+SRR12204850	46	147.47998946649386	33886153	72.88028075905594	9900000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	ribo_initial
+SRR12204851	44	138.35348281341868	15267987	50.06136263288236	4200000000	pass/pass	pass/pass	fail/warn	pass/pass	pass/pass	warn/warn	fail/warn	warn/pass	pass/pass	ribo_initial
+SRR12204734	43.5	147.99665245188368	40570440	54.42737729565836	11900000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/warn	warn/pass	pass/pass	ribo_secondary
+SRR12204735	45	146.69360409051393	23418671	54.75931318038948	6800000000	pass/pass	pass/pass	fail/warn	warn/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	ribo_secondary
+SRR12204847	45	146.45863633896292	20651569	55.788535539030285	6000000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	ribo_secondary
+SRR12204848	47	143.9571233334288	7367597	41.404443710786836	2000000000	pass/pass	pass/pass	fail/warn	pass/pass	pass/pass	warn/warn	warn/warn	warn/pass	pass/pass	ribo_secondary
+SRR12204849	46	147.28598812564456	30832663	63.783125869857734	9000000000	pass/pass	pass/pass	warn/warn	pass/warn	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	ribo_secondary
+SRR12204850	45.5	147.52439800000684	33400914	73.2600030476742	9800000000	pass/pass	pass/pass	warn/warn	pass/pass	pass/pass	warn/warn	fail/fail	warn/pass	pass/pass	ribo_secondary
+SRR12204851	44	138.68851583633503	15097843	50.90426118806289	4000000000	pass/pass	pass/pass	fail/warn	pass/pass	pass/pass	warn/warn	fail/warn	warn/pass	pass/pass	ribo_secondary