Added Rothman enriched notebook

naobservatory · Feb 29, 2024 · 1957271 · 1957271
1 parent 7252fb1
commit 1957271
Show file tree

Hide file tree

Showing 30 changed files with 249,071 additions and 16 deletions.
diff --git a/data/2024-02-29_rothman-2/bracken_counts.tsv b/data/2024-02-29_rothman-2/bracken_counts.tsv
diff --git a/data/2024-02-29_rothman-2/hv_hits_putative_filtered.tsv.gz b/data/2024-02-29_rothman-2/hv_hits_putative_filtered.tsv.gz
diff --git a/data/2024-02-29_rothman-2/qc_adapter_stats.tsv b/data/2024-02-29_rothman-2/qc_adapter_stats.tsv
diff --git a/data/2024-02-29_rothman-2/qc_basic_stats.tsv b/data/2024-02-29_rothman-2/qc_basic_stats.tsv
diff --git a/data/2024-02-29_rothman-2/qc_quality_base_stats.tsv b/data/2024-02-29_rothman-2/qc_quality_base_stats.tsv
diff --git a/data/2024-02-29_rothman-2/qc_quality_sequence_stats.tsv b/data/2024-02-29_rothman-2/qc_quality_sequence_stats.tsv
diff --git a/data/2024-02-29_rothman-2/rothman-libraries-enriched.csv b/data/2024-02-29_rothman-2/rothman-libraries-enriched.csv
@@ -0,0 +1,267 @@
+library,sample_accession,sample
+SRR14530735,SAMN19167898,HTP_9_15_2020
+SRR14530746,SAMN19167897,HTP_9_08_2020
+SRR14530757,SAMN19167896,HTP_9_01_2020
+SRR14530768,SAMN19167895,HTP_8_25_2020
+SRR14530773,SAMN19167944,SJ_9_30_2020
+SRR14530774,SAMN19167943,SJ_9_16_2020
+SRR14530775,SAMN19167942,SJ_9_09_2020
+SRR14530776,SAMN19167941,SJ_9_02_2020
+SRR14530777,SAMN19167940,SJ_8_26_2020
+SRR14530778,SAMN19167939,SJ_8_19_2020
+SRR14530779,SAMN19167894,HTP_8_18_2020
+SRR14530780,SAMN19167938,SJ_8_12_2020
+SRR14530781,SAMN19167937,SJ_10_28_2020
+SRR14530782,SAMN19167936,SJ_10_21_2020
+SRR14530783,SAMN19167935,SJ_10_14_2020
+SRR14530784,SAMN19167934,SJ_10_07_2020
+SRR14530785,SAMN19167933,SB_9_24_2020
+SRR14530786,SAMN19167932,SB_9_10_2020
+SRR14530787,SAMN19167931,SB_8_27_2020
+SRR14530788,SAMN19167930,SB_8_13_2020
+SRR14530789,SAMN19167929,SB_10_22_2020
+SRR14530790,SAMN19167893,HTP_8_11_2020
+SRR14530791,SAMN19167928,PL_9_24_2020
+SRR14530792,SAMN19167927,PL_9_10_2020
+SRR14530793,SAMN19167926,PL_8_27_2020
+SRR14530794,SAMN19167925,PL_8_13_2020
+SRR14530795,SAMN19167924,PL_10_22_2020
+SRR14530796,SAMN19167923,OC_9_30_2020
+SRR14530797,SAMN19167922,OC_9_23_2020
+SRR14530798,SAMN19167921,OC_9_16_2020
+SRR14530799,SAMN19167920,OC_9_03_2020
+SRR14530800,SAMN19167919,OC_9_02_2020
+SRR14530801,SAMN19167892,HTP_10_27_2020
+SRR14530802,SAMN19167918,OC_8_26_2020
+SRR14530803,SAMN19167917,OC_8_19_2020
+SRR14530804,SAMN19167916,OC_8_12_2020
+SRR14530805,SAMN19167915,OC_10_07_2020
+SRR14530806,SAMN19167914,NC_9_11_2020
+SRR14530807,SAMN19167913,NC_8_28_2020
+SRR14530808,SAMN19167912,NC_8_14_2020
+SRR14530809,SAMN19167911,NC_10_23_2020
+SRR14530810,SAMN19167910,NC_10_09_2020
+SRR14530811,SAMN19167909,JWPCP_9_22_2020
+SRR14530812,SAMN19167891,HTP_10_20_2020
+SRR14530813,SAMN19167908,JWPCP_9_15_2020
+SRR14530814,SAMN19167907,JWPCP_9_08_2020
+SRR14530815,SAMN19168068,SJ_9_23_2020
+SRR14530816,SAMN19168067,SJ_11_4_2020
+SRR14530817,SAMN19168066,SJ_11_18_2020
+SRR14530818,SAMN19167899,JW_10_20_2020
+SRR14530819,SAMN19167890,HTP_10_13_2020
+SRR14530820,SAMN19167889,HTP_10_02_2020
+SRR14530821,SAMN19168065,SJ_11_11_2020
+SRR14530822,SAMN19168064,SB_11_5_2020
+SRR14530823,SAMN19168063,SB_10_08_2020
+SRR14530824,SAMN19168062,PL_12_28_2020
+SRR14530825,SAMN19168061,PL_12_22_2020
+SRR14530826,SAMN19168060,PL_12_14_2020
+SRR14530827,SAMN19168059,PL_11_5_2020
+SRR14530828,SAMN19167906,JWPCP_9_01_2020
+SRR14530829,SAMN19168058,PL_11_30_2020
+SRR14530830,SAMN19168057,PL_11_29_2020
+SRR14530831,SAMN19168056,PL_01_04_2021
+SRR14530832,SAMN19168055,PL_01_03_2021
+SRR14530833,SAMN19168054,OC_12_21_2020
+SRR14530834,SAMN19168053,OC_12_14_2020
+SRR14530835,SAMN19168052,OC_11_4_2020
+SRR14530836,SAMN19168051,OC_11_11_2020
+SRR14530837,SAMN19168050,JWPCP_9_29_2020
+SRR14530838,SAMN19168049,JWPCP_11_3_2020
+SRR14530839,SAMN19167905,JWPCP_8_25_2020
+SRR14530840,SAMN19168048,JWPCP_11_17_2020
+SRR14530841,SAMN19168047,JWPCP_11_10_2020
+SRR14530842,SAMN19168046,HTP_9_29_2020
+SRR14530843,SAMN19168045,HTP_9_22_2020
+SRR14530844,SAMN19168044,HTP_12_29_2020
+SRR14530845,SAMN19168043,HTP_12_22_2020
+SRR14530846,SAMN19168042,HTP_12_04_2020
+SRR14530847,SAMN19168041,HTP_11_3_2020
+SRR14530848,SAMN19168040,HTP_11_24_2020
+SRR14530849,SAMN19168039,HTP_01_03_2021
+SRR14530850,SAMN19167904,JWPCP_8_18_2020
+SRR14530861,SAMN19167903,JWPCP_8_11_2020
+SRR14530872,SAMN19167902,JWPCP_10_13_2020
+SRR14530883,SAMN19167901,JWPCP_10_06_2020
+SRR14530894,SAMN19167900,JW_10_27_2020
+SRR18340958,SAMN26732535,HTP_4_8_2021
+SRR18340959,SAMN26732534,HTP_4_6_2021
+SRR18340960,SAMN26732533,HTP_4_4_2021
+SRR18340961,SAMN26732532,HTP_4_29_2021
+SRR18340962,SAMN26732531,HTP_4_26_2021
+SRR18340963,SAMN26732530,HTP_4_25_2021
+SRR18340964,SAMN26732529,HTP_4_22_2021
+SRR18340965,SAMN26732528,HTP_4_15_2021
+SRR18340966,SAMN26732527,HTP_3_9_21
+SRR18340967,SAMN26732455,ESC_11_16_20
+SRR18340968,SAMN26732526,HTP_3_7_21
+SRR18340969,SAMN26732525,HTP_3_4_21
+SRR18340970,SAMN26732524,HTP_3_31_2021
+SRR18340971,SAMN26732523,HTP_3_30_2021
+SRR18340972,SAMN26732522,HTP_3_29_2021
+SRR18340973,SAMN26732521,HTP_3_25_2021
+SRR18340974,SAMN26732520,HTP_3_23_2021
+SRR18340975,SAMN26732519,HTP_3_21_2021
+SRR18340976,SAMN26732518,HTP_3_2_21
+SRR18340977,SAMN26732517,HTP_3_18_2021
+SRR18340978,SAMN26732454,ESC_10_5_20
+SRR18340979,SAMN26732516,HTP_3_16_21
+SRR18340980,SAMN26732515,HTP_3_14_21
+SRR18340981,SAMN26732514,HTP_3_11_21
+SRR18340982,SAMN26732513,HTP_2_9_21
+SRR18340983,SAMN26732512,HTP_2_7_21
+SRR18340984,SAMN26732511,HTP_2_4_21
+SRR18340985,SAMN26732510,HTP_2_28_21
+SRR18340986,SAMN26732484,ESC_8_10_20
+SRR18340987,SAMN26732483,ESC_7_5_2021
+SRR18340988,SAMN26732482,ESC_7_19_2021
+SRR18340989,SAMN26732481,ESC_7_12_2021
+SRR18340990,SAMN26732480,ESC_6_9_2021
+SRR18340991,SAMN26732479,ESC_6_24_2021
+SRR18340992,SAMN26732478,ESC_6_14_2021
+SRR18340993,SAMN26732477,ESC_5_31_2021
+SRR18340994,SAMN26732450,ESC_1_4_21
+SRR18340995,SAMN26732476,ESC_5_24_2021
+SRR18340996,SAMN26732475,ESC_5_10_2021
+SRR18340997,SAMN26732474,ESC_4_5_2021
+SRR18340998,SAMN26732473,ESC_4_26_2021
+SRR18340999,SAMN26732472,ESC_4_19_2021
+SRR18341000,SAMN26732471,ESC_4_12_2021
+SRR18341001,SAMN26732470,ESC_3_8_2021
+SRR18341002,SAMN26732469,ESC_3_29_2021
+SRR18341003,SAMN26732468,ESC_3_22_2021
+SRR18341004,SAMN26732467,ESC_3_17_2021
+SRR18341005,SAMN26732449,ESC_1_25_21
+SRR18341006,SAMN26732466,ESC_3_1_21
+SRR18341007,SAMN26732465,ESC_2_8_21
+SRR18341008,SAMN26732626,PL_8_3_2021
+SRR18341009,SAMN26732625,PL_7_5_2021
+SRR18341010,SAMN26732624,PL_7_29_2021
+SRR18341011,SAMN26732623,PL_7_25_2021
+SRR18341012,SAMN26732622,PL_7_19_2021
+SRR18341013,SAMN26732621,PL_7_12_2021
+SRR18341014,SAMN26732509,HTP_2_23_21
+SRR18341015,SAMN26732508,HTP_2_21_21
+SRR18341016,SAMN26732507,HTP_2_2_21
+SRR18341017,SAMN26732453,ESC_10_26_20
+SRR18341018,SAMN26732506,HTP_2_18_21
+SRR18341019,SAMN26732505,HTP_2_16_21
+SRR18341020,SAMN26732504,HTP_2_15_21
+SRR18341021,SAMN26732503,HTP_2_10_21
+SRR18341022,SAMN26732502,HTP_1_7_21
+SRR18341023,SAMN26732501,HTP_1_5_21
+SRR18341024,SAMN26732500,HTP_1_31_21
+SRR18341025,SAMN26732499,HTP_1_28_21
+SRR18341026,SAMN26732498,HTP_1_26_21
+SRR18341027,SAMN26732497,HTP_1_24_21
+SRR18341028,SAMN26732452,ESC_10_19_20
+SRR18341029,SAMN26732496,HTP_1_21_21
+SRR18341030,SAMN26732495,HTP_1_19_21
+SRR18341031,SAMN26732494,HTP_1_14_21
+SRR18341032,SAMN26732493,HTP_1_12_21
+SRR18341033,SAMN26732492,HTP_1_10_21
+SRR18341034,SAMN26732491,ESC_9_7_20
+SRR18341035,SAMN26732490,ESC_9_21_20
+SRR18341036,SAMN26732489,ESC_9_14_20
+SRR18341037,SAMN26732488,ESC_8_31_20
+SRR18341038,SAMN26732487,ESC_8_3_20
+SRR18341039,SAMN26732451,ESC_10_12_20
+SRR18341040,SAMN26732486,ESC_8_24_20
+SRR18341041,SAMN26732485,ESC_8_17_20
+SRR18341042,SAMN26732595,PL_3_3_2021
+SRR18341043,SAMN26732594,PL_3_29_2021
+SRR18341044,SAMN26732593,PL_3_28_2021
+SRR18341045,SAMN26732592,PL_3_24_2021
+SRR18341046,SAMN26732591,PL_3_22_2021
+SRR18341047,SAMN26732590,PL_3_21_2021
+SRR18341048,SAMN26732589,PL_3_18_2021
+SRR18341049,SAMN26732588,PL_3_15_2021
+SRR18341050,SAMN26732587,PL_3_14_2021
+SRR18341051,SAMN26732461,ESC_12_28_20
+SRR18341052,SAMN26732586,PL_3_10_2021
+SRR18341053,SAMN26732585,PL_3_1_21
+SRR18341054,SAMN26732584,PL_2_8_21
+SRR18341055,SAMN26732583,PL_2_7_21
+SRR18341056,SAMN26732582,PL_2_3_21
+SRR18341057,SAMN26732581,PL_2_28_21
+SRR18341058,SAMN26732580,PL_2_22_21
+SRR18341059,SAMN26732579,PL_2_21_21
+SRR18341060,SAMN26732578,PL_2_17_21
+SRR18341061,SAMN26732577,PL_2_15_21
+SRR18341062,SAMN26732460,ESC_12_21_20
+SRR18341063,SAMN26732576,PL_2_14_21
+SRR18341064,SAMN26732575,PL_2_10_21
+SRR18341065,SAMN26732574,PL_2_1_21
+SRR18341066,SAMN26732573,PL_1_6_21
+SRR18341067,SAMN26732572,PL_1_31_21
+SRR18341068,SAMN26732571,PL_1_27_21
+SRR18341069,SAMN26732570,PL_1_25_21
+SRR18341070,SAMN26732546,HTP_5_4_2021
+SRR18341071,SAMN26732545,HTP_5_31_2021
+SRR18341072,SAMN26732544,HTP_5_25_2021
+SRR18341073,SAMN26732543,HTP_5_24_2021
+SRR18341074,SAMN26732542,HTP_5_23_2021
+SRR18341075,SAMN26732541,HTP_5_20_2021
+SRR18341076,SAMN26732540,HTP_5_2_2021
+SRR18341077,SAMN26732539,HTP_5_18_2021
+SRR18341078,SAMN26732538,HTP_5_16_2021
+SRR18341079,SAMN26732537,HTP_5_13_2021
+SRR18341080,SAMN26732456,ESC_11_2_20
+SRR18341081,SAMN26732536,HTP_5_11_2021
+SRR18341082,SAMN26732620,PL_6_7_2021
+SRR18341083,SAMN26732619,PL_6_28_2021
+SRR18341084,SAMN26732618,PL_6_21_2021
+SRR18341085,SAMN26732617,PL_6_2_2021
+SRR18341086,SAMN26732464,ESC_2_22_21
+SRR18341087,SAMN26732616,PL_6_14_2021
+SRR18341088,SAMN26732615,PL_5_9_2021
+SRR18341089,SAMN26732614,PL_5_5_2021
+SRR18341090,SAMN26732613,PL_5_4_2021
+SRR18341091,SAMN26732612,PL_5_31_2021
+SRR18341092,SAMN26732611,PL_5_3_2021
+SRR18341093,SAMN26732610,PL_5_24_2021
+SRR18341094,SAMN26732609,PL_5_17_2021
+SRR18341095,SAMN26732608,PL_5_12_2021
+SRR18341096,SAMN26732607,PL_5_10_2021
+SRR18341097,SAMN26732463,ESC_2_15_21
+SRR18341098,SAMN26732606,PL_4_7_2021
+SRR18341099,SAMN26732605,PL_4_5_2021
+SRR18341100,SAMN26732604,PL_4_4_2021
+SRR18341101,SAMN26732603,PL_4_28_2021
+SRR18341102,SAMN26732602,PL_4_26_2021
+SRR18341103,SAMN26732601,PL_4_25_2021
+SRR18341104,SAMN26732600,PL_4_21_2021
+SRR18341105,SAMN26732599,PL_4_14_2021
+SRR18341106,SAMN26732598,PL_3_8_2021
+SRR18341107,SAMN26732597,PL_3_7_2021
+SRR18341108,SAMN26732462,ESC_12_7_20
+SRR18341109,SAMN26732596,PL_3_31_2021
+SRR18341110,SAMN26732569,PL_1_24_21
+SRR18341111,SAMN26732568,PL_1_20_21
+SRR18341112,SAMN26732567,PL_1_18_21
+SRR18341113,SAMN26732459,ESC_12_14_20
+SRR18341114,SAMN26732566,PL_1_17_21
+SRR18341115,SAMN26732565,PL_1_14_21
+SRR18341116,SAMN26732564,PL_1_13_21
+SRR18341117,SAMN26732563,PL_1_12_21
+SRR18341118,SAMN26732562,HTP_7_8_2021
+SRR18341119,SAMN26732561,HTP_7_29_2021
+SRR18341120,SAMN26732560,HTP_7_22_2021
+SRR18341121,SAMN26732559,HTP_7_15_2021
+SRR18341122,SAMN26732558,HTP_7_13_2021
+SRR18341123,SAMN26732557,HTP_7_1_2021
+SRR18341124,SAMN26732458,ESC_11_30_20
+SRR18341125,SAMN26732556,HTP_6_6_2021
+SRR18341126,SAMN26732555,HTP_6_3_2021
+SRR18341127,SAMN26732554,HTP_6_27_2021
+SRR18341128,SAMN26732553,HTP_6_24_2021
+SRR18341129,SAMN26732552,HTP_6_20_2021
+SRR18341130,SAMN26732551,HTP_6_15_2021
+SRR18341131,SAMN26732550,HTP_6_10_2021
+SRR18341132,SAMN26732549,HTP_6_1_2021
+SRR18341133,SAMN26732548,HTP_5_9_2021
+SRR18341134,SAMN26732547,HTP_5_6_2021
+SRR18341135,SAMN26732457,ESC_11_23_20
+SRR18341136,SAMN26732448,ESC_1_18_21
+SRR18341137,SAMN26732447,ESC_1_11_21