Datasets:

depinwang
/

star-alignment-qc-per-sample-v1

site large_stringclasses 10 values	sample large_stringlengths 14 23	group large_stringclasses 2 values	status large_stringclasses 1 value	input_reads int64 19.4M 134M	uniq_mapped_n int64 13M 109M	uniq_mapped_pct float64 22.5 96.1	multi_pct float64 2.64 76	total_mapped_pct float64 85.7 99.2	toomany_pct float64 0.02 0.61	unmapped_short_pct float64 0.71 14.1	unmapped_other_pct float64 0.02 0.53	mismatch_pct float64 0.15 0.63	avg_mapped_len float64 198 299	avg_input_len float64 200 300	splices_total int64 3.9M 93.6M
Adn	D341_iAdnR1_RNA1	Ref	ok	51,800,868	46,927,318	90.59	5.32	95.91	0.12	3.83	0.13	0.37	297.21	300	24,235,326
Adn	D341_pAdnR1_RNA1	Alt	ok	60,014,718	55,903,506	93.15	3.87	97.02	0.08	2.81	0.09	0.28	297.72	300	35,034,059
Adn	D351_iAdnL1_RNA1	Ref	ok	51,046,654	40,933,661	80.19	5.78	85.97	0.09	13.84	0.1	0.44	295.91	300	19,690,683
Adn	D351_iAdnR1_RNA1	Ref	ok	56,994,920	46,546,872	81.67	4.71	86.38	0.08	13.44	0.09	0.42	296.04	300	19,425,028
Adn	D357_p2AdnL1_RNA1	Alt	ok	51,816,546	46,934,375	90.58	5.26	95.84	0.06	4.03	0.07	0.31	297.69	300	31,155,334
Adn	D379_pAdnR1_RNA1	Alt	ok	50,455,473	47,029,673	93.21	3.17	96.38	0.04	3.53	0.05	0.29	297.67	300	27,682,282
Adn	D380_pAdnR1_RNA1	Alt	ok	57,639,892	51,525,838	89.39	4.48	93.87	0.07	5.95	0.11	0.29	297.25	300	32,920,078
Adn	D387_pAdnL1_RNA1	Alt	ok	53,353,808	49,112,196	92.05	3.17	95.22	0.03	4.69	0.05	0.33	297.3	300	27,234,604
Adn	D407_pAdnR1_RNA1	Alt	ok	61,078,292	52,432,656	85.84	8.14	93.98	0.09	5.87	0.05	0.31	296.12	300	47,373,635
Adn	D407_pAdnR2_RNA1	Alt	ok	52,488,122	47,846,736	91.16	3.77	94.93	0.06	4.86	0.15	0.35	296.8	300	25,481,417
Adn	D423_pAdnR1_RNA1	Alt	ok	71,866,545	65,227,809	90.76	5.13	95.89	0.06	3.96	0.09	0.26	298.2	300	42,278,702
Adn	D458_pAdnR1_RNA1	Alt	ok	53,360,170	46,840,824	87.78	5.93	93.71	0.06	6.12	0.11	0.32	297.13	300	30,559,481
Adn	D482_p2AdnR1_RNA1	Alt	ok	62,440,685	49,406,998	79.13	12.98	92.11	0.12	7.63	0.14	0.36	296.39	300	20,593,272
Adn	D486_pAdnL1_RNA1	Alt	ok	67,009,614	56,087,974	83.7	8.51	92.21	0.08	7.5	0.2	0.31	296.58	300	43,879,865
Adn	H014_pAdnL1_RNA1	Alt	ok	49,952,469	45,186,840	90.46	5.64	96.1	0.12	3.64	0.14	0.26	297.55	300	24,789,116
Adn	H018_iAdnR_RNA1	Ref	ok	62,991,454	51,938,999	82.45	10.55	93	0.09	6.8	0.1	0.31	296.98	300	44,070,496
Adn	H032_pAdnL1_RNA1	Alt	ok	34,186,382	29,608,535	86.61	11.31	97.92	0.09	1.93	0.05	0.3	199.11	200	17,408,871
Adn	H032_pAdnL3_RNA1	Alt	ok	30,956,901	27,130,312	87.64	10.41	98.05	0.08	1.83	0.04	0.28	199.18	200	17,924,788
Adn	H043_pAdnL1_RNA1	Alt	ok	55,106,371	47,163,631	85.59	12.38	97.97	0.11	1.85	0.07	0.31	199.1	200	23,566,113
Adn	H070_pAdnL1_RNA2	Alt	ok	62,238,974	59,003,388	94.8	2.78	97.58	0.07	2.25	0.1	0.27	298.21	300	28,569,353
Adn	H070_pAdnR1_RNA2	Alt	ok	57,820,033	54,590,381	94.41	2.78	97.19	0.04	2.68	0.08	0.44	297.89	300	25,895,477
Adn	H072_pAdnL1_RNA1	Alt	ok	34,194,762	30,916,378	90.41	5.95	96.36	0.11	3.31	0.21	0.24	199.18	200	10,125,109
Adn	H077_pAdnL1_RNA1	Alt	ok	32,666,221	26,554,611	81.29	15.09	96.38	0.13	3.36	0.13	0.27	199.26	200	13,044,089
Adn	H083_iAdnR1_RNA1	Ref	ok	41,506,821	31,275,337	75.35	20.39	95.74	0.13	3.8	0.33	0.38	198.88	200	21,736,066
Adn	H100_pAdnL1_RNA1	Alt	ok	33,714,163	29,253,956	86.77	11.06	97.83	0.06	2.04	0.07	0.31	199.18	200	15,565,862
Adn	H117_pAdnL1_RNA1	Alt	ok	52,379,674	45,804,944	87.45	8.94	96.39	0.09	3.44	0.08	0.28	297.7	300	25,658,781
Adn	H123_pAdnR1_RNA1	Alt	ok	56,928,889	50,271,155	88.31	3.29	91.6	0.04	8.3	0.06	0.28	296.83	300	27,362,136
Adn	H131_pAdnR1_RNA1	Alt	ok	47,863,068	45,781,270	95.65	3.03	98.68	0.05	1.17	0.09	0.19	199.57	200	16,392,232
Adn	H133_pAdnL1_RNA1	Alt	ok	54,759,941	46,821,972	85.5	4.97	90.47	0.09	9.15	0.28	0.35	295.5	300	18,751,536
Adn	H142_iAdnR1_RNA3	Ref	ok	37,518,453	32,735,321	87.25	7.78	95.03	0.18	4.66	0.12	0.45	198.47	200	11,575,760
Adn	H213_p2AdnR1_TR_RNA2	Alt	ok	56,687,778	48,862,890	86.2	9.86	96.06	0.2	3.63	0.11	0.43	198.6	200	21,171,564
Adn	H222_pAdnL1_TR_RNA	Alt	ok	52,223,687	45,831,385	87.76	8.82	96.58	0.09	3.26	0.08	0.36	297.7	300	24,452,804
Adn	H229_pAdnR1_TR_RNA2	Alt	ok	66,179,814	54,213,758	81.92	14.49	96.41	0.15	3.35	0.09	0.28	198.72	200	22,231,325
Adn	H243_pAdnR1_RNA1	Alt	ok	71,551,278	56,715,977	79.27	18.36	97.63	0.09	2.21	0.08	0.32	199.17	200	29,888,819
Adn	H245_iAdnL1_RNA1	Ref	ok	67,389,729	56,265,411	83.49	14.04	97.53	0.09	2.33	0.05	0.27	199.13	200	24,628,465
Adn	H245_iAdnR1_RNA2	Ref	ok	57,177,468	50,968,675	89.14	8.57	97.71	0.08	2.13	0.08	0.27	199.26	200	18,757,823
Adn	H259_pAdnL1_RNA1	Alt	ok	52,372,206	46,952,118	89.65	6.84	96.49	0.06	3.36	0.09	0.27	297.57	300	46,550,152
Adn	H261_p2AdnL1_RNA1	Alt	ok	53,456,428	50,164,904	93.84	2.93	96.77	0.04	3.12	0.07	0.38	297.63	300	22,931,658
Adn	H262_pAdnL1_RNA1	Alt	ok	52,421,607	48,557,959	92.63	4.06	96.69	0.05	3.17	0.1	0.29	297.62	300	26,110,223
Adn	H267_pAdnR1_RNA1	Alt	ok	55,055,072	48,816,344	88.67	3.24	91.91	0.1	7.87	0.12	0.45	295.27	300	20,773,876
Adn	H286_pAdnL1_RNA1	Alt	ok	51,951,806	46,406,233	89.33	3.67	93	0.05	6.87	0.09	0.26	296.72	300	27,955,264
Adn	H287_pAdnL1_RNA1	Alt	ok	52,487,786	49,508,700	94.32	3.05	97.37	0.03	2.55	0.04	0.26	297.95	300	31,249,007
Adn	H289_pAdnR1_RNA1	Alt	ok	51,725,866	48,225,030	93.23	3.17	96.4	0.08	3.41	0.12	0.3	297.54	300	24,304,302
Adn	H290_pAdnL1_RNA1	Alt	ok	54,334,614	48,527,984	89.31	3.7	93.01	0.05	6.78	0.16	0.29	296.25	300	28,380,422
Adn	H309_pAdnL1_RNA2	Alt	ok	53,699,572	48,303,899	89.95	6.33	96.28	0.08	3.55	0.08	0.31	297.81	300	30,780,904
Adn	H316_iAdnL1_RNA1	Ref	ok	60,848,013	55,835,768	91.76	4.16	95.92	0.05	3.95	0.08	0.31	297.27	300	31,992,514
Adn	H325_iAdnL1_RNA1	Ref	ok	51,551,080	47,333,983	91.82	4.91	96.73	0.11	3.07	0.09	0.29	297.78	300	25,022,231
Adn	M005_pAdnL1_RNA6	Alt	ok	60,632,054	56,032,148	92.41	4.95	97.36	0.04	2.48	0.12	0.26	298.06	300	32,608,367
Adn	M005_pAdnR1_RNA2	Alt	ok	61,963,967	57,385,965	92.61	4.91	97.52	0.03	2.39	0.06	0.26	298.08	300	41,597,132
Adn	M006_pAdnL1_RNA1	Alt	ok	57,340,694	53,988,932	94.15	3.59	97.74	0.04	2.15	0.07	0.25	298.14	300	39,867,807
Adn	OC023_iAdn1_RNA1	Ref	ok	83,874,127	73,349,051	87.45	8.79	96.24	0.1	3.6	0.06	0.47	198.49	200	33,517,734
Bow	D357_p2Bow1_RNA1	Alt	ok	52,596,187	46,926,895	89.22	5.97	95.19	0.08	4.62	0.11	0.35	297.31	300	30,432,581
Bow	D466_pBow1_RNA1	Alt	ok	52,327,428	45,979,906	87.87	5.12	92.99	0.1	6.77	0.14	0.35	296.85	300	27,426,295
Bow	D474_p2Bow1_RNA1	Alt	ok	67,985,661	50,087,640	73.67	17.41	91.08	0.13	8.68	0.11	0.4	295.96	300	36,261,777
Bow	D479_pBow2_RNA1	Alt	ok	60,784,262	52,146,755	85.79	7.06	92.85	0.08	6.99	0.08	0.31	296.87	300	29,155,254
Bow	D483_p2Bow1_RNA1	Alt	ok	71,491,645	50,612,992	70.8	20.85	91.65	0.19	8.06	0.1	0.35	296.27	300	26,735,322
Bow	H052_r1Bow1_RNA2	Alt	ok	51,122,643	46,819,607	91.58	4.08	95.66	0.06	4.05	0.23	0.34	297.14	300	22,415,437
Bow	H082_pBow1_RNA1	Alt	ok	49,254,069	45,542,029	92.46	3.82	96.28	0.07	3.57	0.08	0.27	297.65	300	26,637,096
Bow	H086_iBow2_RNA1	Ref	ok	50,883,726	45,579,071	89.57	6.94	96.51	0.04	3.38	0.06	0.23	297.76	300	32,421,410
Bow	H099_pBow1_RNA1	Alt	ok	49,927,096	46,550,508	93.24	3.35	96.59	0.1	3.24	0.07	0.25	297.73	300	36,120,653
Bow	H151_p2Bow2_RNA1	Alt	ok	52,537,506	47,543,199	90.49	6.52	97.01	0.08	2.82	0.09	0.31	297.92	300	31,088,127
Bow	H166_iBow2_RNA1	Ref	ok	63,273,442	54,657,800	86.38	9.26	95.64	0.12	4.16	0.08	0.41	198.45	200	30,870,575
Bow	H185_iBow1_RNA1	Ref	ok	60,637,659	54,447,047	89.79	6.07	95.86	0.1	3.9	0.14	0.37	198.61	200	18,825,402
Bow	H194_iBow1_RNA1	Ref	ok	47,455,765	41,590,485	87.64	8.16	95.8	0.13	3.92	0.15	0.41	198.55	200	16,316,227
Bow	H210_p2Bow1_c_RNA2	Alt	ok	49,908,134	43,799,585	87.76	6.68	94.44	0.08	5.41	0.07	0.27	296.88	300	32,016,919
Bow	H210_r1Bow1_RNA1	Alt	ok	53,831,682	48,907,952	90.85	4.74	95.59	0.05	4.24	0.11	0.27	297.31	300	23,611,921
Bow	H222_pBow1_RNA1	Alt	ok	60,200,076	55,747,013	92.6	4.04	96.64	0.06	3.25	0.05	0.26	297.87	300	37,876,958
Bow	H250_pBow1_RNA1	Alt	ok	52,769,505	48,981,259	92.82	4.21	97.03	0.06	2.8	0.1	0.29	297.82	300	30,282,567
Bow	H271_pBow1_RNA1	Alt	ok	51,660,066	48,129,564	93.17	3.55	96.72	0.07	3.13	0.08	0.3	297.62	300	31,113,282
Bow	H322_pBow1_RNA1	Alt	ok	56,866,135	50,968,265	89.63	6.72	96.35	0.09	3.49	0.08	0.33	297.75	300	31,674,110
LN	D339_pLNL1_RNA1	Alt	ok	79,986,268	72,233,910	90.31	5.04	95.35	0.06	4.4	0.19	0.27	297.18	300	36,487,241
LN	D380_pLNR1_RNA1	Alt	ok	54,288,150	47,626,689	87.73	5.38	93.11	0.08	6.66	0.16	0.27	297.32	300	29,736,148
LN	D398_pLN2_RNA1	Alt	ok	50,715,124	47,403,128	93.47	3.63	97.1	0.04	2.82	0.05	0.22	297.82	300	36,009,244
LN	D407_pLNL1_RNA1	Alt	ok	91,135,788	84,447,837	92.66	3.39	96.05	0.05	3.81	0.09	0.31	297.33	300	52,842,032
LN	D423_pLNL1_RNA1	Alt	ok	60,768,931	55,735,533	91.72	4.86	96.58	0.05	3.27	0.1	0.27	298.22	300	30,430,455
LN	D473_pLN1_RNA1	Alt	ok	65,579,748	56,633,396	86.36	6.9	93.26	0.06	6.48	0.2	0.31	296.93	300	21,036,976
LN	D474_p2LN1_RNA1	Alt	ok	52,063,998	47,037,441	90.35	6.74	97.09	0.03	2.84	0.05	0.3	298.15	300	29,938,698
LN	D481_p2LN1_RNA1	Alt	ok	61,545,644	51,047,887	82.94	12.11	95.05	0.1	4.74	0.1	0.31	297.31	300	34,088,960
LN	D486_pLN1_RNA1	Alt	ok	59,942,395	48,863,844	81.52	10.49	92.01	0.11	7.75	0.14	0.33	296.43	300	27,033,122
LN	H024_pLNR1_RNA2	Alt	ok	47,419,388	39,771,834	83.87	14.06	97.93	0.07	1.95	0.05	0.42	198.98	200	22,130,126
LN	H024_pLNR2_RNA1	Alt	ok	55,079,907	45,528,322	82.66	15.74	98.4	0.05	1.51	0.04	0.29	199.17	200	27,726,211
LN	H033_pLN1_RNA2	Alt	ok	59,390,542	50,973,909	85.83	11.65	97.48	0.07	2.32	0.13	0.36	198.98	200	17,338,721
LN	H043_pLNL1_RNA1	Alt	ok	40,534,657	33,210,624	81.93	16.65	98.58	0.07	1.29	0.06	0.33	199.27	200	19,469,208
LN	H081_pLNR1_RNA1	Alt	ok	46,309,299	38,704,831	83.58	14.39	97.97	0.06	1.87	0.1	0.33	199.02	200	21,669,145
LN	H129_iLNR1_RNA1	Ref	ok	54,114,427	49,812,352	92.05	5.1	97.15	0.04	2.69	0.12	0.31	297.86	300	21,072,422
LN	H177_pLNR1_xO_RNA1	Alt	ok	83,942,237	77,169,083	91.93	5.7	97.63	0.02	2.22	0.12	0.32	199.14	200	44,708,202
LN	H224_r1LNR1_RNA2	Ref	ok	51,421,491	47,120,211	91.64	5.49	97.13	0.05	2.78	0.05	0.27	298.04	300	26,014,139
LN	H248_pLNL2_RNA1	Alt	ok	52,824,529	48,668,321	92.13	4.89	97.02	0.05	2.83	0.11	0.28	297.99	300	26,327,954
LN	H248_pLNR1_RNA1	Alt	ok	50,179,522	45,284,271	90.24	7.05	97.29	0.04	2.62	0.05	0.25	298.26	300	40,819,128
LN	H248_pLNR1_RNA1_set8	Alt	ok	67,071,773	53,140,433	79.23	18.25	97.48	0.09	2.38	0.04	0.3	198.7	200	35,193,211
LN	H267_pLNL4_RNA1	Alt	ok	49,396,754	35,016,587	70.89	24.47	95.36	0.12	4.46	0.06	0.39	198.11	200	20,671,704
LN	OC038_r1LN1_RNA1	Ref	ok	86,464,011	81,731,255	94.53	3.41	97.94	0.08	1.9	0.08	0.31	199.34	200	38,193,672
Plf	H248_r1Plf1_RNA1	Ref	ok	50,605,736	44,504,034	87.94	9.11	97.05	0.07	2.8	0.09	0.26	298.14	300	42,197,707
Plf	H325_pPlf1_RNA1	Alt	ok	53,220,314	45,351,414	85.21	11.67	96.88	0.13	2.9	0.08	0.28	298.07	300	43,059,478
Plf	D327_r1PlfL1_RNA1	Ref	ok	50,600,674	46,666,982	92.23	3.57	95.8	0.03	4.12	0.06	0.22	297.68	300	43,969,739
Plf	D335_r1Plf1_RNA1	Ref	ok	52,913,012	47,688,252	90.13	5.7	95.83	0.04	4.1	0.03	0.26	297.7	300	40,263,841
Plf	H284_pPlf1_RNA1	Alt	ok	54,005,346	45,503,613	84.26	9.74	94	0.06	5.89	0.05	0.33	297.21	300	33,801,388
Plf	H276_r1PlfR1_RNA1	Ref	ok	55,983,078	51,446,530	91.9	3.96	95.86	0.04	4.05	0.05	0.32	297.3	300	47,332,168
Plf	H259_r1Plf1_RNA1	Ref	ok	77,027,363	59,403,193	77.12	15.48	92.6	0.16	7.07	0.17	0.26	297.58	300	59,097,126
Plf	H297_r1Plf1_RNA1	Ref	ok	55,272,963	45,005,551	81.42	11.62	93.04	0.12	6.71	0.12	0.25	297.68	300	43,570,051

End of preview. Expand in Data Studio

star-alignment-qc-per-sample-v1

Per-sample STAR 2nd-pass alignment metrics for 1048 aligned ovarian-cancer RNA-seq samples (10 sites), parsed from Log.final.out. Uniq-mapped median 89.2%, total mapped median 96.4%, mismatch/base max 0.63%; 31 samples uniq<70% (high multi-mapping).

Dataset Info

Rows: 1048
Columns: 18

Columns

Column	Type	Description
site	Value('large_string')	Anatomical site (Adn/Asc/Bow/LN/Mes/Ome/Ovary/Per/Plf/Tub).
sample	Value('large_string')	Sample identifier (canonical name).
group	Value('large_string')	rMATS group label (Ref/Alt) from the per-site experiment.tsv.
status	Value('large_string')	Parse status; 'ok' for all 1048.
input_reads	Value('int64')	STAR: number of input read pairs.
uniq_mapped_n	Value('int64')	STAR: uniquely mapped reads number.
uniq_mapped_pct	Value('float64')	STAR: uniquely mapped reads % (primary alignment rate).
multi_pct	Value('float64')	STAR: % of reads mapped to multiple loci.
total_mapped_pct	Value('float64')	uniq_mapped_pct + multi_pct (total aligned %).
toomany_pct	Value('float64')	STAR: % of reads mapped to too many loci.
unmapped_short_pct	Value('float64')	STAR: % unmapped because too short.
unmapped_other_pct	Value('float64')	STAR: % unmapped, other.
unmapped_mismatch_pct	Value('float64')	STAR: % unmapped, too many mismatches.
mismatch_pct	Value('float64')	STAR: mismatch rate per base, % (alignment quality).
avg_mapped_len	Value('float64')	STAR: average mapped length.
avg_input_len	Value('float64')	STAR: average input read length.
chimeric_pct	Value('float64')	STAR: % chimeric reads.
splices_total	Value('int64')	STAR: total number of splices.

Generation Parameters

{
  "script_name": "01_parse_star_logs.py",
  "description": "Per-sample STAR 2nd-pass alignment metrics for 1048 aligned ovarian-cancer RNA-seq samples (10 sites), parsed from Log.final.out. Uniq-mapped median 89.2%, total mapped median 96.4%, mismatch/base max 0.63%; 31 samples uniq<70% (high multi-mapping).",
  "model": "n/a (STAR log parsing)",
  "experiment_name": "star-alignment-qc",
  "cluster": "ePouta",
  "artifact_status": "final",
  "canary": false,
  "input_datasets": [],
  "hyperparameters": {}
}

Usage

from datasets import load_dataset

dataset = load_dataset("depinwang/star-alignment-qc-per-sample-v1", split="train")
print(f"Loaded {len(dataset)} rows")

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