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1 <tool id="cshl_fastx_quality_statistics_ng" name="Compute quality statistics">
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2 <description>(improved)</description>
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3 <command>
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4 cat '$input' |
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5 fastx_quality_stats
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6 #if $input.ext == "fastqsanger":
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7 -Q 33
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8 #elif $input.ext == "fastq":
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9 -Q 64
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10 #end if
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11 -N -o '$output'
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12 </command>
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13
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14 <inputs>
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15 <param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to analyse" />
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16 </inputs>
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17
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18 <tests>
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19 <test>
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20 <param name="input" value="fastq_stats1.fastq" />
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21 <output name="output" file="fastq_stats1.out" />
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22 </test>
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23 </tests>
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24
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25 <outputs>
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26 <data format="tabular" name="output" metadata_source="input"
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27 />
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28 </outputs>
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29
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30 <help>
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31
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32 **What it does**
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33
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34 Creates quality statistics report for the given Solexa/FASTQ library.
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35
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36 .. class:: warningmark
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37
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38 The output format is different than the old quality statistics tool. It can't be used for the quality-chart and nucleotide distribution tools (without further processing)
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39
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40 -----
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41
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42 **The output file will contain the following fields:**
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43
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44 * cycle = cycle number (1 to 36 for a 36-cycles read solexa file)
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45 * max-count = maximum number of bases (in all cycles)
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46
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47 For each nucleotide type of each cycle (ALL/A/C/G/T/N), the following columns are generated:
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48
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49 * count = number of bases found in this column.
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50 * min = Lowest quality score value found in this column.
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51 * max = Highest quality score value found in this column.
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52 * sum = Sum of quality score values for this column.
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53 * mean = Mean quality score value for this column.
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54 * Q1 = 1st quartile quality score.
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55 * med = Median quality score.
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56 * Q3 = 3rd quartile quality score.
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57 * IQR = Inter-Quartile range (Q3-Q1).
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58 * lW = 'Left-Whisker' value (for boxplotting).
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59 * rW = 'Right-Whisker' value (for boxplotting).
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60
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61
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62 (see column list at the bottom of this page)
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63
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64 -----
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65
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66 **Output Example**::
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67
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68 cycle max_count ALL_count ALL_min ALL_max ALL_sum ALL_mean ALL_Q1 ALL_med ALL_Q3 ALL_IQR ALL_lW ALL_rW A_count A_min A_max A_sum A_mean A_Q1 A_med A_Q3 A_IQR A_lW A_rW C_count C_min C_max C_sum C_mean C_Q1 C_med C_Q3 C_IQR C_lW C_rW G_count G_min G_max G_sum G_mean G_Q1 G_med G_Q3 G_IQR G_lW G_rW T_count T_min T_max T_sum T_mean T_Q1 T_med T_Q3 T_IQR T_lW T_rW N_count N_min N_max N_sum N_mean N_Q1 N_med N_Q3 N_IQR N_lW N_rW
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69 1 2827201 2827201 5 34 86622739 30.64 33 33 33 0 33 33 31337 5 34 841248 26.85 23 30 33 10 8 34 9269 5 34 154582 16.68 5 12 30 25 5 34 2095406 5 34 64401991 30.73 33 33 33 0 33 33 689133 5 34 21214602 30.78 33 33 33 0 33 33 2056 5 13 10316 5.02 5 5 5 0 5 5
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70 2 2827201 2827201 5 34 81416729 28.80 27 33 33 6 18 34 1860337 5 34 56188709 30.20 33 33 33 0 33 33 21274 5 34 420221 19.75 11 21 30 19 5 34 862406 5 34 22835654 26.48 21 32 33 12 5 34 81979 5 34 1964575 23.96 17 26 33 16 5 34 1205 5 24 7570 6.28 5 5 5 0 5 5
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71 3 2827201 2827201 5 34 89142476 31.53 33 33 34 1 32 34 18121 5 34 203489 11.23 5 5 15 10 5 30 45699 5 34 944362 20.66 5 26 33 28 5 34 79472 5 34 859251 10.81 5 5 12 7 5 22 2682082 5 34 87126165 32.48 33 33 34 1 32 34 1827 5 18 9209 5.04 5 5 5 0 5 5
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72 4 2827201 2827201 5 34 90033575 31.85 33 34 34 1 32 34 172281 5 34 2905831 16.87 5 11 33 28 5 34 2597111 5 34 85653490 32.98 33 34 34 1 32 34 24461 5 34 643275 26.30 23 33 33 10 8 34 32749 5 34 827798 25.28 17 33 33 16 5 34 599 5 21 3181 5.31 5 5 5 0 5 5
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73 5 2827201 2827201 5 34 89641650 31.71 33 33 34 1 32 34 26774 5 34 476388 17.79 5 13 33 28 5 34 58691 5 34 891506 15.19 5 5 32 27 5 34 54916 5 34 714335 13.01 5 5 24 19 5 34 2685062 5 34 87550414 32.61 33 33 34 1 32 34 1758 5 21 9007 5.12 5 5 5 0 5 5
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74 6 2827201 2827201 5 34 84595812 29.92 29 33 33 4 23 34 1204450 5 34 36229599 30.08 29 33 33 4 23 34 463119 5 34 13924930 30.07 30 33 33 3 26 34 712076 5 34 21093763 29.62 28 33 33 5 21 34 447508 5 34 13347178 29.83 29 33 33 4 23 34 48 5 21 342 7.12 5 5 7 2 5 10
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75 7 2827201 2827201 5 34 81404399 28.79 26 33 33 7 16 34 912751 5 34 26241597 28.75 26 33 33 7 16 34 540022 5 34 15843612 29.34 28 33 33 5 21 34 701269 5 34 19699830 28.09 26 32 33 7 16 34 672893 5 34 19617405 29.15 27 33 33 6 18 34 266 5 24 1955 7.35 5 5 7 2 5 10
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76 8 2827201 2827201 5 34 83714332 29.61 28 33 33 5 21 34 809852 5 34 23610246 29.15 27 33 33 6 18 34 563842 5 34 17062600 30.26 30 33 33 3 26 34 650887 5 34 18848062 28.96 27 33 33 6 18 34 802551 5 34 24192911 30.15 30 33 33 3 26 34 69 5 24 513 7.43 5 5 5 0 5 5
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77 9 2827201 2827201 5 34 83974872 29.70 28 33 33 5 21 34 834129 5 34 24483965 29.35 27 33 33 6 18 34 567059 5 34 17270502 30.46 30 33 33 3 26 34 620453 5 34 17917829 28.88 26 33 33 7 16 34 805499 5 34 24302177 30.17 30 33 33 3 26 34 61 5 26 399 6.54 5 5 5 0 5 5
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78 10 2827201 2827201 5 34 83278375 29.46 27 33 33 6 18 34 896783 5 34 26245652 29.27 27 33 33 6 18 34 551055 5 34 16628773 30.18 30 33 33 3 26 34 648328 5 34 18502443 28.54 26 33 33 7 16 34 730957 5 34 21900963 29.96 30 33 33 3 26 34 78 5 21 544 6.97 5 5 7 2 5 10
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79 11 2827201 2827201 5 34 82511316 29.18 27 33 33 6 18 34 857880 5 34 24789241 28.90 27 33 33 6 18 34 642205 5 34 19342469 30.12 30 33 33 3 26 34 655942 5 34 18484775 28.18 26 31 33 7 16 34 671046 5 34 19893945 29.65 28 33 33 5 21 34 128 5 24 886 6.92 5 5 5 0 5 5
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80 12 2827201 2827201 5 34 83171736 29.42 27 33 33 6 18 34 826807 5 34 24025084 29.06 27 33 33 6 18 34 586948 5 34 17775697 30.28 30 33 33 3 26 34 636734 5 34 17999923 28.27 26 31 33 7 16 34 776614 5 34 23370369 30.09 30 33 33 3 26 34 98 5 18 663 6.77 5 5 5 0 5 5
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81 13 2827201 2827201 5 34 82829608 29.30 27 33 33 6 18 34 822607 5 34 23762719 28.89 27 33 33 6 18 34 644718 5 34 19458385 30.18 30 33 33 3 26 34 591437 5 34 16607859 28.08 26 31 33 7 16 34 768323 5 34 22999812 29.94 30 33 33 3 26 34 116 5 24 833 7.18 5 5 7 2 5 10
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82 14 2827201 2827201 5 34 82345826 29.13 27 33 33 6 18 34 798164 5 34 22982673 28.79 26 33 33 7 16 34 649845 5 34 19506688 30.02 30 33 33 3 26 34 608966 5 34 16892044 27.74 24 31 33 9 11 34 770051 5 34 22963200 29.82 29 33 33 4 23 34 175 5 24 1221 6.98 5 5 5 0 5 5
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83 15 2827201 2827201 5 34 82462892 29.17 27 33 33 6 18 34 831167 5 34 23971929 28.84 26 33 33 7 16 34 613017 5 34 18416386 30.04 30 33 33 3 26 34 621149 5 34 17284205 27.83 24 31 33 9 11 34 761767 5 34 22789700 29.92 29 33 33 4 23 34 101 5 18 672 6.65 5 5 5 0 5 5
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84 16 2827201 2827201 5 34 82526664 29.19 27 33 33 6 18 34 824933 5 34 23753705 28.79 26 33 33 7 16 34 610126 5 34 18388479 30.14 30 33 33 3 26 34 612088 5 34 16999148 27.77 24 31 33 9 11 34 779925 5 34 23384436 29.98 30 33 33 3 26 34 129 5 24 896 6.95 5 5 5 0 5 5
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85 17 2827201 2827201 5 34 82610038 29.22 27 33 33 6 18 34 819008 5 34 23665033 28.89 27 33 33 6 18 34 618277 5 34 18651436 30.17 30 33 33 3 26 34 597414 5 34 16501609 27.62 24 30 33 9 11 34 792381 5 34 23791076 30.02 30 33 33 3 26 34 121 5 21 884 7.31 5 5 5 0 5 5
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86 18 2827201 2827201 5 34 82402647 29.15 27 33 33 6 18 34 815170 5 34 23471377 28.79 26 33 33 7 16 34 615913 5 34 18527086 30.08 30 33 33 3 26 34 607020 5 34 16707257 27.52 24 30 33 9 11 34 788977 5 34 23695988 30.03 30 33 33 3 26 34 121 5 24 939 7.76 5 5 11 6 5 20
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87 19 2827201 2827201 5 34 82124647 29.05 27 33 33 6 18 34 799663 5 34 22872641 28.60 26 32 33 7 16 34 628535 5 34 18876510 30.03 30 33 33 3 26 34 610246 5 34 16776560 27.49 24 30 33 9 11 34 788629 5 34 23598027 29.92 29 33 33 4 23 34 128 5 27 909 7.10 5 5 5 0 5 5
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88 20 2827201 2827201 5 34 81985110 29.00 27 33 33 6 18 34 797587 5 34 22834667 28.63 26 32 33 7 16 34 636494 5 34 19081110 29.98 30 33 33 3 26 34 603916 5 34 16456404 27.25 24 30 33 9 11 34 789056 5 34 23611835 29.92 29 33 33 4 23 34 148 5 27 1094 7.39 5 5 7 2 5 10
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89 21 2827201 2827201 5 34 81789492 28.93 27 33 33 6 18 34 794078 5 34 22654429 28.53 26 32 33 7 16 34 636334 5 34 19008271 29.87 29 33 33 4 23 34 614943 5 34 16761297 27.26 24 30 33 9 11 34 781661 5 34 23364202 29.89 29 33 33 4 23 34 185 5 27 1293 6.99 5 5 5 0 5 5
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90 22 2827201 2827201 5 34 81451811 28.81 27 33 33 6 18 34 789032 5 34 22366485 28.35 26 31 33 7 16 34 645777 5 34 19277917 29.85 29 33 33 4 23 34 608030 5 34 16404902 26.98 23 29 33 10 8 34 784198 5 34 23401407 29.84 29 33 33 4 23 34 164 5 24 1100 6.71 5 5 5 0 5 5
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91 23 2827201 2827201 5 34 80945146 28.63 26 32 33 7 16 34 786207 5 34 22128593 28.15 26 31 33 7 16 34 647440 5 34 19187231 29.64 28 33 33 5 21 34 607663 5 34 16274550 26.78 22 29 33 11 6 34 785744 5 34 23353803 29.72 29 33 33 4 23 34 147 5 24 969 6.59 5 5 5 0 5 5
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92 24 2827201 2827201 5 34 80501327 28.47 26 32 33 7 16 34 786929 5 34 22067207 28.04 26 31 33 7 16 34 645831 5 34 19042366 29.49 28 33 33 5 21 34 612772 5 34 16261175 26.54 22 29 33 11 6 34 781496 5 34 23129334 29.60 28 33 33 5 21 34 173 5 26 1245 7.20 5 5 5 0 5 5
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93 25 2827201 2827201 5 34 79714527 28.20 26 31 33 7 16 34 782000 5 34 21701186 27.75 24 30 33 9 11 34 644171 5 34 18796511 29.18 27 33 33 6 18 34 617490 5 34 16226119 26.28 22 28 33 11 6 34 783396 5 34 22989588 29.35 27 33 33 6 18 34 144 5 26 1123 7.80 5 5 11 6 5 20
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94 26 2827201 2827201 5 34 77523225 27.42 24 31 33 9 11 34 783881 5 34 21162231 27.00 24 30 33 9 11 34 645075 5 34 18368273 28.47 27 33 33 6 18 34 617885 5 34 15635967 25.31 21 27 33 12 5 34 779368 5 34 22349766 28.68 27 33 33 6 18 34 992 5 27 6988 7.04 5 5 5 0 5 5
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95 27 2827201 2827201 5 34 76792679 27.16 24 31 33 9 11 34 788575 5 34 21113021 26.77 23 30 33 10 8 34 638456 5 34 18023093 28.23 26 32 33 7 16 34 624665 5 34 15600176 24.97 21 27 33 12 5 34 774483 5 34 22049478 28.47 27 32 33 6 18 34 1022 5 27 6911 6.76 5 5 5 0 5 5
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96 28 2827201 2827201 5 34 76446203 27.04 24 30 33 9 11 34 783001 5 34 20828394 26.60 22 30 33 11 6 34 639424 5 34 17921638 28.03 26 32 33 7 16 34 621361 5 34 15437055 24.84 21 27 33 12 5 34 782313 5 34 22251729 28.44 27 32 33 6 18 34 1102 5 26 7387 6.70 5 5 5 0 5 5
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97 29 2827201 2827201 5 34 75869397 26.84 24 30 33 9 11 34 777718 5 34 20485923 26.34 22 30 33 11 6 34 645283 5 34 18004108 27.90 26 31 33 7 16 34 627295 5 34 15440771 24.61 21 27 33 12 5 34 775728 5 34 21930783 28.27 26 32 33 7 16 34 1177 5 27 7812 6.64 5 5 5 0 5 5
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98 30 2827201 2827201 5 34 75137420 26.58 22 30 33 11 6 34 779313 5 34 20336426 26.10 22 29 33 11 6 34 646974 5 34 17887122 27.65 24 31 33 9 11 34 626980 5 34 15205903 24.25 19 26 33 14 5 34 772774 5 34 21699992 28.08 26 31 33 7 16 34 1160 5 27 7977 6.88 5 5 5 0 5 5
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99 31 2827201 2827201 5 34 74256817 26.27 22 30 33 11 6 34 780211 5 34 20171360 25.85 21 29 33 12 5 34 645371 5 34 17606830 27.28 24 31 33 9 11 34 629456 5 34 14997599 23.83 18 26 33 15 5 34 771023 5 34 21473316 27.85 26 31 33 7 16 34 1140 5 27 7712 6.76 5 5 5 0 5 5
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100 32 2827201 2827201 5 34 73624704 26.04 22 29 33 11 6 34 776741 5 34 19802248 25.49 21 28 33 12 5 34 642994 5 34 17408712 27.07 24 30 33 9 11 34 631699 5 34 14925494 23.63 18 26 32 14 5 34 774316 5 34 21478972 27.74 26 31 33 7 16 34 1451 5 27 9278 6.39 5 5 5 0 5 5
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101 33 2827201 2827201 5 34 72833249 25.76 21 29 33 12 5 34 775426 5 34 19509710 25.16 21 27 33 12 5 34 644177 5 34 17265182 26.80 24 30 33 9 11 34 627490 5 34 14612407 23.29 18 26 31 13 5 34 778476 5 34 21435400 27.54 24 31 33 9 11 34 1632 5 27 10550 6.46 5 5 5 0 5 5
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102 34 2827201 2827201 5 34 71937995 25.44 21 28 33 12 5 34 772803 5 34 19226676 24.88 21 27 33 12 5 34 647127 5 34 17098061 26.42 22 30 33 11 6 34 628686 5 34 14382900 22.88 17 24 31 14 5 34 777289 5 34 21221307 27.30 24 30 33 9 11 34 1296 5 27 9051 6.98 5 5 5 0 5 5
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103 35 2827201 2827201 5 34 70604895 24.97 21 27 33 12 5 34 769554 5 34 18722160 24.33 19 27 32 13 5 34 643915 5 34 16662802 25.88 21 28 33 12 5 34 627642 5 34 14115224 22.49 17 24 30 13 5 34 784712 5 34 21095775 26.88 24 30 33 9 11 34 1378 5 27 8934 6.48 5 5 5 0 5 5
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104 36 2827201 2827201 5 34 71705284 25.36 21 28 33 12 5 34 775278 5 34 18770248 24.21 18 27 33 15 5 34 634906 5 34 16703972 26.31 22 30 33 11 6 34 630819 5 34 14421307 22.86 17 24 31 14 5 34 784826 5 34 21800547 27.78 26 32 33 7 16 34 1372 5 27 9210 6.71 5 5 5 0 5 5
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105
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106 -----
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107
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108 All columns::
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109
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110 cycle
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111 max_count
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112 ALL_count
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113 ALL_min
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114 ALL_max
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115 ALL_sum
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116 ALL_mean
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117 ALL_Q1
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118 ALL_med
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119 ALL_Q3
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120 ALL_IQR
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121 ALL_lW
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122 ALL_rW
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123 A_count
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124 A_min
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125 A_max
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126 A_sum
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127 A_mean
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128 A_Q1
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129 A_med
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130 A_Q3
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131 A_IQR
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132 A_lW
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133 A_rW
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134 C_count
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135 C_min
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136 C_max
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137 C_sum
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138 C_mean
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139 C_Q1
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140 C_med
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141 C_Q3
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142 C_IQR
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143 C_lW
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144 C_rW
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145 G_count
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146 G_min
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147 G_max
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148 G_sum
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149 G_mean
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150 G_Q1
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151 G_med
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152 G_Q3
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153 G_IQR
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154 G_lW
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155 G_rW
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156 T_count
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157 T_min
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158 T_max
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159 T_sum
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160 T_mean
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161 T_Q1
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162 T_med
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163 T_Q3
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164 T_IQR
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165 T_lW
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166 T_rW
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167 N_count
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168 N_min
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169 N_max
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170 N_sum
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171 N_mean
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172 N_Q1
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173 N_med
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174 N_Q3
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175 N_IQR
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176 N_lW
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177 N_rW
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178
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179 ------
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180
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181 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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182
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183 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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184
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185 </help>
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186 </tool>
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187 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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