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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty
author mheinzl
date Wed, 14 Aug 2019 12:38:15 -0400
parents c825a29a7d9f
children 6651e76baca1
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Values from family size distribution with all datasets (tags)

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 (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	0.339	0.420	0.325
SSCS ba	59	222	0.488	0.481	0.476	0.468
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
	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

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	0.339	0.420	0.325
SSCS ba	59	222	0.488	0.481	0.476	0.468
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
	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

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	0.339	0.420	0.325
SSCS ba	59	222	0.488	0.481	0.476	0.468
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
	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

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	0.339	0.420	0.325
SSCS ba	59	222	0.488	0.481	0.476	0.468
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
	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