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

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
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9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1 hd_data.tab
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2 nr of tags 20
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3 sample size 20
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4
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5 Hamming distance separated by family size
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6 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
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7 HD=1 5 1 1 1 1 0 9
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8 HD=6 3 0 0 0 0 0 3
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9 HD=7 4 0 0 0 1 0 5
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10 HD=8 2 0 0 1 0 0 3
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11 sum 14 1 1 2 2 0 20
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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13 Family size distribution separated by Hamming distance
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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14 HD=1 HD=2 HD=3 HD=4 HD=5-8 HD>8 sum
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15 FS=1 5 0 0 0 9 0 14
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16 FS=2 1 0 0 0 0 0 1
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17 FS=3 1 0 0 0 0 0 1
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18 FS=4 1 0 0 0 1 0 2
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19 FS=6 1 0 0 0 0 0 1
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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20 FS=7 0 0 0 0 1 0 1
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21 sum 9 0 0 0 11 0 20
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24 max. family size in sample: 7
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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25 absolute frequency: 1
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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26 relative frequency: 0.05
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9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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28 The Hamming distances were calculated by comparing the first halve against all halves and selected the minimum value (HD a).
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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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').
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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30 Finally, it was possible to calculate the absolute and relative differences between the HDs (absolute and relative delta HD).
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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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.
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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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.
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34 length of one half of the tag 12
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36 Hamming distance of each half in the tag
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37 HD DCS HD b' HD b HD a' HD a+b', a'+b sum
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38 HD=0 20 0 8 1 0 29
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39 HD=1 0 0 1 19 8 28
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40 HD=2 0 0 0 0 1 1
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41 HD=5 0 0 3 0 0 3
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42 HD=6 0 0 2 0 3 5
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43 HD=7 0 1 6 0 4 11
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44 HD=8 0 2 0 0 7 9
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45 HD=9 0 1 0 0 1 2
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46 HD=10 0 2 0 0 2 4
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47 HD=11 0 7 0 0 7 14
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48 HD=12 0 7 0 0 7 14
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49 sum 20 20 20 20 40 120
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50
29
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51 Absolute delta Hamming distance within the tag
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52 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
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53 diff=7 1 0 0 0 0 0 1
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54 diff=8 1 0 0 0 1 0 2
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55 diff=9 1 0 0 0 0 0 1
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56 diff=10 2 0 0 0 0 0 2
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57 diff=11 4 0 1 1 1 0 7
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58 diff=12 5 1 0 1 0 0 7
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59 sum 14 1 1 2 2 0 20
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60
29
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61 Chimera analysis: relative delta Hamming distance
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62 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
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63 diff=1.0 14 1 1 2 2 0 20
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64 sum 14 1 1 2 2 0 20
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65
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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.
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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67 So the Hamming distances of the chimeric tags are shown.
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68 Hamming distance of chimeric families separated after FS
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69 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
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70 HD=7 1 0 0 0 0 0 1
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71 HD=8 1 0 0 0 1 0 2
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72 HD=9 1 0 0 0 0 0 1
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73 HD=10 2 0 0 0 0 0 2
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74 HD=11 4 0 1 1 1 0 7
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75 HD=12 5 1 0 1 0 0 7
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76 sum 14 1 1 2 2 0 20
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77
29
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78 Hamming distance of chimeric families separated after DCS and single SSCS
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79 DCS SSCS ab SSCS ba sum
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 25
diff changeset
80 HD=7.0 0 0 1 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 25
diff changeset
81 HD=8.0 0 1 1 2
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 25
diff changeset
82 HD=9.0 0 1 0 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 25
diff changeset
83 HD=10.0 0 1 1 2
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 25
diff changeset
84 HD=11.0 0 3 4 7
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 25
diff changeset
85 HD=12.0 0 2 5 7
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 25
diff changeset
86 sum 0 8 12 20
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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87
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 25
diff changeset
88