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comparison test-data/hd_output.tab @ 29:6b15b3b6405c draft

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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
author mheinzl
date Wed, 24 Jul 2019 05:58:15 -0400
parents 9e384b0741f1
children
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28:1fa7342a140d 29:6b15b3b6405c
1 hd_data.tab 1 hd_data.tab
2 number of tags per file 20 (from 20) against 20 2 nr of tags 20
3 sample size 20
3 4
4 Hamming distance separated by family size 5 Hamming distance separated by family size
5 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum 6 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
6 HD=1 5 1 1 1 1 0 9 7 HD=1 5 1 1 1 1 0 9
7 HD=6 3 0 0 0 0 0 3 8 HD=6 3 0 0 0 0 0 3
27 The Hamming distances were calculated by comparing the first halve against all halves and selected the minimum value (HD a). 28 The Hamming distances were calculated by comparing the first halve against all halves and selected the minimum value (HD a).
28 For the second half of the tag, we compared them against all tags which resulted in the minimum HD of the previous step and selected the maximum value (HD b'). 29 For the second half of the tag, we compared them against all tags which resulted in the minimum HD of the previous step and selected the maximum value (HD b').
29 Finally, it was possible to calculate the absolute and relative differences between the HDs (absolute and relative delta HD). 30 Finally, it was possible to calculate the absolute and relative differences between the HDs (absolute and relative delta HD).
30 These calculations were repeated, but starting with the second half in the first step to find all possible chimeras in the data (HD b and HD For simplicity we used the maximum value between the delta values in the end. 31 These calculations were repeated, but starting with the second half in the first step to find all possible chimeras in the data (HD b and HD For simplicity we used the maximum value between the delta values in the end.
31 When only tags that can form DCS were allowed in the analysis, family sizes for the forward and reverse (ab and ba) will be included in the plots. 32 When only tags that can form DCS were allowed in the analysis, family sizes for the forward and reverse (ab and ba) will be included in the plots.
32 length of one part of the tag = 12 33
34 length of one half of the tag 12
33 35
34 Hamming distance of each half in the tag 36 Hamming distance of each half in the tag
35 HD a HD b' HD b HD a' HD a+b sum 37 HD DCS HD b' HD b HD a' HD a+b', a'+b sum
36 HD=0 20 0 8 1 0 29 38 HD=0 20 0 8 1 0 29
37 HD=1 0 0 1 19 8 28 39 HD=1 0 0 1 19 8 28
38 HD=2 0 0 0 0 1 1 40 HD=2 0 0 0 0 1 1
39 HD=5 0 0 3 0 0 3 41 HD=5 0 0 3 0 0 3
40 HD=6 0 0 2 0 3 5 42 HD=6 0 0 2 0 3 5
44 HD=10 0 2 0 0 2 4 46 HD=10 0 2 0 0 2 4
45 HD=11 0 7 0 0 7 14 47 HD=11 0 7 0 0 7 14
46 HD=12 0 7 0 0 7 14 48 HD=12 0 7 0 0 7 14
47 sum 20 20 20 20 40 120 49 sum 20 20 20 20 40 120
48 50
49 Absolute delta Hamming distances within the tag 51 Absolute delta Hamming distance within the tag
50 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum 52 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
51 diff=7 1 0 0 0 0 0 1 53 diff=7 1 0 0 0 0 0 1
52 diff=8 1 0 0 0 1 0 2 54 diff=8 1 0 0 0 1 0 2
53 diff=9 1 0 0 0 0 0 1 55 diff=9 1 0 0 0 0 0 1
54 diff=10 2 0 0 0 0 0 2 56 diff=10 2 0 0 0 0 0 2
55 diff=11 4 0 1 1 1 0 7 57 diff=11 4 0 1 1 1 0 7
56 diff=12 5 1 0 1 0 0 7 58 diff=12 5 1 0 1 0 0 7
57 sum 14 1 1 2 2 0 20 59 sum 14 1 1 2 2 0 20
58 60
59 Chimera analysis: relative delta Hamming distances 61 Chimera analysis: relative delta Hamming distance
60 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum 62 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
61 diff=1.0 14 1 1 2 2 0 20 63 diff=1.0 14 1 1 2 2 0 20
62 sum 14 1 1 2 2 0 20 64 sum 14 1 1 2 2 0 20
63 65
64 Chimeras:
65 All tags were filtered: only those tags where at least one half was identical (HD=0) and therefore, had a relative delta of 1 were kept. These tags are considered as chimeric. 66 All tags were filtered: only those tags where at least one half was identical (HD=0) and therefore, had a relative delta of 1 were kept. These tags are considered as chimeric.
66 So the Hamming distances of the chimeric tags are shown. 67 So the Hamming distances of the chimeric tags are shown.
67 Hamming distances of chimeras 68 Hamming distance of chimeric families separated after FS
68 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum 69 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
69 HD=7 1 0 0 0 0 0 1 70 HD=7 1 0 0 0 0 0 1
70 HD=8 1 0 0 0 1 0 2 71 HD=8 1 0 0 0 1 0 2
71 HD=9 1 0 0 0 0 0 1 72 HD=9 1 0 0 0 0 0 1
72 HD=10 2 0 0 0 0 0 2 73 HD=10 2 0 0 0 0 0 2
73 HD=11 4 0 1 1 1 0 7 74 HD=11 4 0 1 1 1 0 7
74 HD=12 5 1 0 1 0 0 7 75 HD=12 5 1 0 1 0 0 7
75 sum 14 1 1 2 2 0 20 76 sum 14 1 1 2 2 0 20
76 77
78 Hamming distance of chimeric families separated after DCS and single SSCS
79 DCS SSCS ab SSCS ba sum
80 HD=7.0 0 0 1 1
81 HD=8.0 0 1 1 2
82 HD=9.0 0 1 0 1
83 HD=10.0 0 1 1 2
84 HD=11.0 0 3 4 7
85 HD=12.0 0 2 5 7
86 sum 0 8 12 20
77 87
88