ccbr1187 data run

[kopardev]

Description of feature

Run real project data from ccbr1187

[kelly-sovacool]

first run completed, but will re-run with v0.2.0

[kelly-sovacool]

running in /data/CCBR/projects/ccbr1187/CHAMPAGNE_v0.2.0 on biowulf

champagne init
champagne run --mode local --input samplesheet.csv --genome mm10 -preview
champagne run --mode slurm --input samplesheet.csv --genome mm10

[kelly-sovacool]

Comparing read counts to old pipeliner:

SampleName	name	value_orig	value_new	rel_diff_percent
D1_Input_1	NReads	204412055	408824110	100.00
D1_Input_1	NMappedReads	349471104	350597036	0.32
D1_Input_1	NUniqMappedReads	257039206	257799730	0.30
D1_Input_2	NReads	226555465	453110930	100.00
D1_Input_2	NMappedReads	386415459	387629277	0.31
D1_Input_2	NUniqMappedReads	286596196	287446152	0.30
D1_P7+TLX3_STAT5_1	NReads	72630765	145261530	100.00
D1_P7+TLX3_STAT5_1	NMappedReads	120574446	120938735	0.30
D1_P7+TLX3_STAT5_1	NUniqMappedReads	84420590	84675786	0.30
D1_P7+TLX3_STAT5_2	NReads	70185244	140370488	100.00
D1_P7+TLX3_STAT5_2	NMappedReads	117360597	117725501	0.31
D1_P7+TLX3_STAT5_2	NUniqMappedReads	84018510	84258946	0.29
D1_P7+TLX3_TLX3_1	NReads	64765059	129530118	100.00
D1_P7+TLX3_TLX3_1	NMappedReads	105354661	105703353	0.33
D1_P7+TLX3_TLX3_1	NUniqMappedReads	71413146	71643278	0.32
D1_P7+TLX3_TLX3_2	NReads	64838609	129677218	100.00
D1_P7+TLX3_TLX3_2	NMappedReads	107182187	107525051	0.32
D1_P7+TLX3_TLX3_2	NUniqMappedReads	75891666	76122192	0.30
D1_P7+TLX3_TLX3_Input_3	NReads	211456008	422912016	100.00
D1_P7+TLX3_TLX3_Input_3	NMappedReads	351106840	352200524	0.31
D1_P7+TLX3_TLX3_Input_3	NUniqMappedReads	259883902	260614698	0.28
D1_P7+TLX3_TLX3_Input_4	NReads	208845700	417691400	100.00
D1_P7+TLX3_TLX3_Input_4	NMappedReads	349017095	350089273	0.31
D1_P7+TLX3_TLX3_Input_4	NUniqMappedReads	260652520	261399180	0.29
D1_STAT5_1	NReads	73454435	146908870	100.00
D1_STAT5_1	NMappedReads	125567570	125983941	0.33
D1_STAT5_1	NUniqMappedReads	87170772	87452850	0.32
D1_STAT5_2	NReads	63886275	127772550	100.00
D1_STAT5_2	NMappedReads	109588855	109952094	0.33
D1_STAT5_2	NUniqMappedReads	76737298	76980324	0.32
D1_TLX3_1	NReads	63979497	127958994	100.00
D1_TLX3_1	NMappedReads	109400016	109757618	0.33
D1_TLX3_1	NUniqMappedReads	77164758	77403410	0.31
D1_TLX3_2	NReads	59299793	118599586	100.00
D1_TLX3_2	NMappedReads	101453518	101781981	0.32
D1_TLX3_2	NUniqMappedReads	72115790	72337222	0.31

working dir: /data/CCBR/projects/ccbr1187/champagne_2023-10-30

[kelly-sovacool]

Peak counts are lower than they should be for this dataset, but seem fine for the mm10 test data.

ccbr1187

sample_id	tool	count_old	count_new	rel_diff_percent
D1_P7+TLX3_STAT5_1	gem	4337	2233	-48.51
D1_P7+TLX3_STAT5_2	gem	1303	807	-38.07
D1_P7+TLX3_TLX3_1	gem	1373	869	-36.71
D1_P7+TLX3_TLX3_2	gem	1281	581	-54.64
D1_STAT5_1	gem	2723	1223	-55.09
D1_STAT5_2	gem	1179	663	-43.77
D1_TLX3_1	gem	977	795	-18.63
D1_TLX3_2	gem	1190	771	-35.21
D1_P7+TLX3_STAT5_1	macs_broad	2223	210	-90.55
D1_P7+TLX3_STAT5_2	macs_broad	491	143	-70.88
D1_P7+TLX3_TLX3_1	macs_broad	113	19	-83.19
D1_P7+TLX3_TLX3_2	macs_broad	160	20	-87.50
D1_STAT5_1	macs_broad	18171	157	-99.14
D1_STAT5_2	macs_broad	392	131	-66.58
D1_TLX3_1	macs_broad	422	2	-99.53
D1_TLX3_2	macs_broad	114	6	-94.74
D1_P7+TLX3_STAT5_1	macs_narrow	2075	178	-91.42
D1_P7+TLX3_STAT5_2	macs_narrow	467	124	-73.45
D1_P7+TLX3_TLX3_1	macs_narrow	114	14	-87.72
D1_P7+TLX3_TLX3_2	macs_narrow	145	14	-90.34
D1_STAT5_1	macs_narrow	15231	126	-99.17
D1_STAT5_2	macs_narrow	372	107	-71.24
D1_TLX3_1	macs_narrow	372	2	-99.46
D1_TLX3_2	macs_narrow	91	5	-94.51
D1_P7+TLX3_STAT5_1	sicer	43949	66942	52.32
D1_P7+TLX3_STAT5_2	sicer	18063	35309	95.48
D1_P7+TLX3_TLX3_1	sicer	17267	32213	86.56
D1_P7+TLX3_TLX3_2	sicer	16871	34259	103.06
D1_STAT5_1	sicer	45753	51428	12.40
D1_STAT5_2	sicer	25164	29108	15.67
D1_TLX3_1	sicer	31466	36199	15.04
D1_TLX3_2	sicer	28301	43853	54.95

full_mm10

sample_id	tool	count_old	count_new	rel_diff_percent
CTCF_ChIP_macrophage_p20_1	gem	73312	71726	-2.16
CTCF_ChIP_macrophage_p20_2	gem	67761	66106	-2.44
CTCF_ChIP_macrophage_p3_1	gem	67253	68263	1.50
CTCF_ChIP_macrophage_p3_2	gem	61301	60183	-1.82
CTCF_ChIP_MEF_p20_1	gem	77060	76071	-1.28
CTCF_ChIP_MEF_p20_2	gem	76964	76743	-0.29
CTCF_ChIP_macrophage_p20_1	macs_broad	56990	58429	2.53
CTCF_ChIP_macrophage_p20_2	macs_broad	60203	62555	3.91
CTCF_ChIP_macrophage_p3_1	macs_broad	51693	52165	0.91
CTCF_ChIP_macrophage_p3_2	macs_broad	61916	62704	1.27
CTCF_ChIP_MEF_p20_1	macs_broad	61936	62873	1.51
CTCF_ChIP_MEF_p20_2	macs_broad	74418	72367	-2.76
CTCF_ChIP_macrophage_p20_1	macs_narrow	59628	58951	-1.14
CTCF_ChIP_macrophage_p20_2	macs_narrow	63839	63380	-0.72
CTCF_ChIP_macrophage_p3_1	macs_narrow	53750	52524	-2.28
CTCF_ChIP_macrophage_p3_2	macs_narrow	62470	62422	-0.08
CTCF_ChIP_MEF_p20_1	macs_narrow	64913	63444	-2.26
CTCF_ChIP_MEF_p20_2	macs_narrow	78729	73261	-6.95
CTCF_ChIP_macrophage_p20_1	sicer	63953	63965	0.02
CTCF_ChIP_macrophage_p20_2	sicer	57660	53414	-7.36
CTCF_ChIP_macrophage_p3_1	sicer	57696	51590	-10.58
CTCF_ChIP_macrophage_p3_2	sicer	69919	60339	-13.70
CTCF_ChIP_MEF_p20_1	sicer	59309	61538	3.76
CTCF_ChIP_MEF_p20_2	sicer	60055	68593	14.22