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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit 9bae9043a53f1e07b502acd1082450adcb6d9e31-dirty
author mheinzl
date Wed, 16 Oct 2019 10:07:17 -0400
parents e51fe3083b16
children
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Values from family size distribution with all datasets based on families

Family size	fsd_data1.tab	fsd_data2.tab	fsd_data3.tab	fsd_data4.tab
FS=1	63	63	63	63	
FS=2	5	5	5	5	
FS=3	8	8	8	8	
FS=4	9	9	9	9	
FS=5	3	3	3	3	
FS=6	5	5	5	5	
FS=7	3	3	3	3	
FS=8	3	3	3	3	
FS=9	2	2	2	2	
FS=10	3	3	3	3	
FS=11	1	1	1	1	
FS=12	3	3	3	3	
FS=13	3	3	3	3	
FS=14	0	0	0	0	
FS=15	0	0	0	0	
FS=16	0	0	0	0	
FS=17	0	0	0	0	
FS=18	0	0	0	0	
FS=19	0	0	0	0	
FS=20	0	0	0	0	
FS>20	1	1	1	1	
sum	112	112	112	112	

Values from family size distribution with all datasets based on PE reads

Family size	fsd_data1.tab	fsd_data2.tab	fsd_data3.tab	fsd_data4.tab
FS=1	63	63	63	63	
FS=2	10	10	10	10	
FS=3	24	24	24	24	
FS=4	36	36	36	36	
FS=5	15	15	15	15	
FS=6	30	30	30	30	
FS=7	21	21	21	21	
FS=8	24	24	24	24	
FS=9	18	18	18	18	
FS=10	30	30	30	30	
FS=11	11	11	11	11	
FS=12	36	36	36	36	
FS=13	39	39	39	39	
FS=14	0	0	0	0	
FS=15	0	0	0	0	
FS=16	0	0	0	0	
FS=17	0	0	0	0	
FS=18	0	0	0	0	
FS=19	0	0	0	0	
FS=20	0	0	0	0	
FS>20	21	21	21	21	
sum	378	378	378	378	

Dataset:	fsd_data1.tab
max. family size:	21
absolute frequency:	1
relative frequency:	0.009

median family size:	1.0
mean family size:	3.375

	singletons:			family size > 20:				length of dataset:
	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
fsd_data1.tab	63	0.562	0.167	1	0.009	21	0.056	112	378

The unique frequencies were calculated from the dataset where the tags occured only once (=ab without DCS, ba without DCS)
Whereas the total frequencies were calculated from the whole dataset (=including the DCS).

FS >= 1	nr. of tags	nr. of PE reads	rel. freq of tags		rel. freq of PE reads:
			unique:	total	unique	total:
SSCS ab	47	123	0.431	0.420	0.339	0.325
SSCS ba	59	222	0.541	0.527	0.612	0.587
DCS (total)	3 (6)	18 (33)	0.028	0.027 (0.054)	0.050	0.048 (0.087)
total nr. of tags	109	363	109	112	363	378

FS >= 3	nr. of tags	nr. of PE reads	rel. freq of tags		rel. freq of PE reads:
			unique:	total	unique	total:
SSCS ab	14	87	0.341	0.259	0.313	0.224
SSCS ba	26	187	0.491	0.481	0.495	0.482
DCS (total)	1 (2)	4 (14)	0.024	0.024 (0.048)	0.014	0.014 (0.049)
total nr. of tags	41	278	41	42	278	288

Values from family size distribution based on families
	duplex	ab	ba	sum
FS=1	2	30	31	63
FS=2	0	3	2	5
FS=3	0	3	5	8
FS=4	2	3	4	9
FS=5	0	2	1	3
FS=6	0	1	4	5
FS=7	0	1	2	3
FS=8	0	1	2	3
FS=9	0	0	2	2
FS=10	1	1	1	3
FS=11	0	0	1	1
FS=12	0	1	2	3
FS=13	1	1	1	3
FS=14	0	0	0	0
FS=15	0	0	0	0
FS=16	0	0	0	0
FS=17	0	0	0	0
FS=18	0	0	0	0
FS=19	0	0	0	0
FS=20	0	0	0	0
FS>20	0	0	1	1
sum	6	47	59	112

Values from family size distribution based on PE reads
	duplex	ab	ba	sum
FS=1	2	30	31	63
FS=2	0	6	4	10
FS=3	0	9	15	24
FS=4	8	12	16	36
FS=5	0	10	5	15
FS=6	0	6	24	30
FS=7	0	7	14	21
FS=8	0	8	16	24
FS=9	0	0	18	18
FS=10	10	10	10	30
FS=11	0	0	11	11
FS=12	0	12	24	36
FS=13	13	13	13	39
FS=14	0	0	0	0
FS=15	0	0	0	0
FS=16	0	0	0	0
FS=17	0	0	0	0
FS=18	0	0	0	0
FS=19	0	0	0	0
FS=20	0	0	0	0
FS>20	0	0	21	21
sum	33	123	222	378

Dataset:	fsd_data2.tab
max. family size:	21
absolute frequency:	1
relative frequency:	0.009

median family size:	1.0
mean family size:	3.375

	singletons:			family size > 20:				length of dataset:
	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
fsd_data2.tab	63	0.562	0.167	1	0.009	21	0.056	112	378

The unique frequencies were calculated from the dataset where the tags occured only once (=ab without DCS, ba without DCS)
Whereas the total frequencies were calculated from the whole dataset (=including the DCS).

FS >= 1	nr. of tags	nr. of PE reads	rel. freq of tags		rel. freq of PE reads:
			unique:	total	unique	total:
SSCS ab	47	123	0.431	0.420	0.339	0.325
SSCS ba	59	222	0.541	0.527	0.612	0.587
DCS (total)	3 (6)	18 (33)	0.028	0.027 (0.054)	0.050	0.048 (0.087)
total nr. of tags	109	363	109	112	363	378

FS >= 3	nr. of tags	nr. of PE reads	rel. freq of tags		rel. freq of PE reads:
			unique:	total	unique	total:
SSCS ab	14	87	0.341	0.259	0.313	0.224
SSCS ba	26	187	0.491	0.481	0.495	0.482
DCS (total)	1 (2)	4 (14)	0.024	0.024 (0.048)	0.014	0.014 (0.049)
total nr. of tags	41	278	41	42	278	288

Values from family size distribution based on families
	duplex	ab	ba	sum
FS=1	2	30	31	63
FS=2	0	3	2	5
FS=3	0	3	5	8
FS=4	2	3	4	9
FS=5	0	2	1	3
FS=6	0	1	4	5
FS=7	0	1	2	3
FS=8	0	1	2	3
FS=9	0	0	2	2
FS=10	1	1	1	3
FS=11	0	0	1	1
FS=12	0	1	2	3
FS=13	1	1	1	3
FS=14	0	0	0	0
FS=15	0	0	0	0
FS=16	0	0	0	0
FS=17	0	0	0	0
FS=18	0	0	0	0
FS=19	0	0	0	0
FS=20	0	0	0	0
FS>20	0	0	1	1
sum	6	47	59	112

Values from family size distribution based on PE reads
	duplex	ab	ba	sum
FS=1	2	30	31	63
FS=2	0	6	4	10
FS=3	0	9	15	24
FS=4	8	12	16	36
FS=5	0	10	5	15
FS=6	0	6	24	30
FS=7	0	7	14	21
FS=8	0	8	16	24
FS=9	0	0	18	18
FS=10	10	10	10	30
FS=11	0	0	11	11
FS=12	0	12	24	36
FS=13	13	13	13	39
FS=14	0	0	0	0
FS=15	0	0	0	0
FS=16	0	0	0	0
FS=17	0	0	0	0
FS=18	0	0	0	0
FS=19	0	0	0	0
FS=20	0	0	0	0
FS>20	0	0	21	21
sum	33	123	222	378

Dataset:	fsd_data3.tab
max. family size:	21
absolute frequency:	1
relative frequency:	0.009

median family size:	1.0
mean family size:	3.375

	singletons:			family size > 20:				length of dataset:
	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
fsd_data3.tab	63	0.562	0.167	1	0.009	21	0.056	112	378

The unique frequencies were calculated from the dataset where the tags occured only once (=ab without DCS, ba without DCS)
Whereas the total frequencies were calculated from the whole dataset (=including the DCS).

FS >= 1	nr. of tags	nr. of PE reads	rel. freq of tags		rel. freq of PE reads:
			unique:	total	unique	total:
SSCS ab	47	123	0.431	0.420	0.339	0.325
SSCS ba	59	222	0.541	0.527	0.612	0.587
DCS (total)	3 (6)	18 (33)	0.028	0.027 (0.054)	0.050	0.048 (0.087)
total nr. of tags	109	363	109	112	363	378

FS >= 3	nr. of tags	nr. of PE reads	rel. freq of tags		rel. freq of PE reads:
			unique:	total	unique	total:
SSCS ab	14	87	0.341	0.259	0.313	0.224
SSCS ba	26	187	0.491	0.481	0.495	0.482
DCS (total)	1 (2)	4 (14)	0.024	0.024 (0.048)	0.014	0.014 (0.049)
total nr. of tags	41	278	41	42	278	288

Values from family size distribution based on families
	duplex	ab	ba	sum
FS=1	2	30	31	63
FS=2	0	3	2	5
FS=3	0	3	5	8
FS=4	2	3	4	9
FS=5	0	2	1	3
FS=6	0	1	4	5
FS=7	0	1	2	3
FS=8	0	1	2	3
FS=9	0	0	2	2
FS=10	1	1	1	3
FS=11	0	0	1	1
FS=12	0	1	2	3
FS=13	1	1	1	3
FS=14	0	0	0	0
FS=15	0	0	0	0
FS=16	0	0	0	0
FS=17	0	0	0	0
FS=18	0	0	0	0
FS=19	0	0	0	0
FS=20	0	0	0	0
FS>20	0	0	1	1
sum	6	47	59	112

Values from family size distribution based on PE reads
	duplex	ab	ba	sum
FS=1	2	30	31	63
FS=2	0	6	4	10
FS=3	0	9	15	24
FS=4	8	12	16	36
FS=5	0	10	5	15
FS=6	0	6	24	30
FS=7	0	7	14	21
FS=8	0	8	16	24
FS=9	0	0	18	18
FS=10	10	10	10	30
FS=11	0	0	11	11
FS=12	0	12	24	36
FS=13	13	13	13	39
FS=14	0	0	0	0
FS=15	0	0	0	0
FS=16	0	0	0	0
FS=17	0	0	0	0
FS=18	0	0	0	0
FS=19	0	0	0	0
FS=20	0	0	0	0
FS>20	0	0	21	21
sum	33	123	222	378

Dataset:	fsd_data4.tab
max. family size:	21
absolute frequency:	1
relative frequency:	0.009

median family size:	1.0
mean family size:	3.375

	singletons:			family size > 20:				length of dataset:
	nr. of tags	rel. freq of tags	rel.freq of PE reads	nr. of tags	rel. freq of tags	nr. of PE reads	rel. freq of PE reads	total nr. of tags	total nr. of PE reads
fsd_data4.tab	63	0.562	0.167	1	0.009	21	0.056	112	378

The unique frequencies were calculated from the dataset where the tags occured only once (=ab without DCS, ba without DCS)
Whereas the total frequencies were calculated from the whole dataset (=including the DCS).

FS >= 1	nr. of tags	nr. of PE reads	rel. freq of tags		rel. freq of PE reads:
			unique:	total	unique	total:
SSCS ab	47	123	0.431	0.420	0.339	0.325
SSCS ba	59	222	0.541	0.527	0.612	0.587
DCS (total)	3 (6)	18 (33)	0.028	0.027 (0.054)	0.050	0.048 (0.087)
total nr. of tags	109	363	109	112	363	378

FS >= 3	nr. of tags	nr. of PE reads	rel. freq of tags		rel. freq of PE reads:
			unique:	total	unique	total:
SSCS ab	14	87	0.341	0.259	0.313	0.224
SSCS ba	26	187	0.491	0.481	0.495	0.482
DCS (total)	1 (2)	4 (14)	0.024	0.024 (0.048)	0.014	0.014 (0.049)
total nr. of tags	41	278	41	42	278	288

Values from family size distribution based on families
	duplex	ab	ba	sum
FS=1	2	30	31	63
FS=2	0	3	2	5
FS=3	0	3	5	8
FS=4	2	3	4	9
FS=5	0	2	1	3
FS=6	0	1	4	5
FS=7	0	1	2	3
FS=8	0	1	2	3
FS=9	0	0	2	2
FS=10	1	1	1	3
FS=11	0	0	1	1
FS=12	0	1	2	3
FS=13	1	1	1	3
FS=14	0	0	0	0
FS=15	0	0	0	0
FS=16	0	0	0	0
FS=17	0	0	0	0
FS=18	0	0	0	0
FS=19	0	0	0	0
FS=20	0	0	0	0
FS>20	0	0	1	1
sum	6	47	59	112

Values from family size distribution based on PE reads
	duplex	ab	ba	sum
FS=1	2	30	31	63
FS=2	0	6	4	10
FS=3	0	9	15	24
FS=4	8	12	16	36
FS=5	0	10	5	15
FS=6	0	6	24	30
FS=7	0	7	14	21
FS=8	0	8	16	24
FS=9	0	0	18	18
FS=10	10	10	10	30
FS=11	0	0	11	11
FS=12	0	12	24	36
FS=13	13	13	13	39
FS=14	0	0	0	0
FS=15	0	0	0	0
FS=16	0	0	0	0
FS=17	0	0	0	0
FS=18	0	0	0	0
FS=19	0	0	0	0
FS=20	0	0	0	0
FS>20	0	0	21	21
sum	33	123	222	378