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annotate test-data/fastqc_customlimits.txt @ 14:f2e8552cf1d0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
author iuc
date Mon, 23 Oct 2017 13:26:32 -0400
parents a00a6402d09a
children 3e1cdf5406db
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a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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1 # For each of the modules you can choose to not run that
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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2 # module at all by setting the value below to 1 for the
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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3 # modules you want to remove.
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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4 duplication ignore 1
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5 kmer ignore 0
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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6 n_content ignore 0
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7 overrepresented ignore 0
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8 quality_base ignore 0
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9 sequence ignore 0
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10 gc_sequence ignore 0
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11 quality_sequence ignore 1
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12 tile ignore 1
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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13 sequence_length ignore 0
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14 adapter ignore 0
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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15
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16 # For the duplication module the value is the percentage
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17 # remaining after deduplication. Measured levels below
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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18 # these limits trigger the warning / error.
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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19 duplication warn 70
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20 duplication error 50
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21
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22 # For the kmer module the filter is on the -log10 binomial
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23 # pvalue for the most significant Kmer, so 5 would be
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24 # 10^-5 = p<0.00001
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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25 kmer warn 2
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26 kmer error 5
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27
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28 # For the N module the filter is on the percentage of Ns
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29 # at any position in the library
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30 n_content warn 5
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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31 n_content error 20
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32
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33 # For the overrepresented seqs the warn value sets the
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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34 # threshold for the overrepresented sequences to be reported
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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35 # at all as the proportion of the library which must be seen
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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36 # as a single sequence
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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37 overrepresented warn 0.001
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38 overrepresented error 1
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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39
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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40 # The per base quality filter uses two values, one for the value
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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41 # of the lower quartile, and the other for the value of the
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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42 # median quality. Failing either of these will trigger the alert
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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43 quality_base_lower warn 10
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44 quality_base_lower error 5
a00a6402d09a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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45 quality_base_median warn 50
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46 quality_base_median error 20
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47
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48 # The per base sequence content module tests the maximum deviation
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49 # between A and T or C and G
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50 sequence warn 2
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51 sequence error 5
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52
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53 # The per sequence GC content tests the maximum deviation between
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54 # the theoretical distribution and the real distribution
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55 gc_sequence warn 15
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56 gc_sequence error 30
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57
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58 # The per sequence quality module tests the phred score which is
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59 # most frequently observed
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60 quality_sequence warn 27
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61 quality_sequence error 20
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62
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63 # The per tile module tests the maximum phred score loss between
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64 # and individual tile and the average for that base across all tiles
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65 tile warn 5
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66 tile error 10
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67
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68 # The sequence length module tests are binary, so the values here
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69 # simply turn them on or off. The actual tests warn if you have
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70 # sequences of different length, and error if you have sequences
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71 # of zero length.
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72
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73 sequence_length warn 1
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74 sequence_length error 1
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75
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76 # The adapter module's warnings and errors are based on the
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77 # percentage of reads in the library which have been observed
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78 # to contain an adapter associated Kmer at any point
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79
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80 adapter warn 5
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81 adapter error 10
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82
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