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annotate test-data/fastqc_customlimits.txt @ 17:7b0207bd2183 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2f544e337886709995a93d53f394919ce8e4673a
author iuc
date Fri, 10 May 2019 14:23:28 -0400
parents 92d9da2a738d
children 7d3cef9c42ca
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5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
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1 # For each of the modules you can choose to not run that
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
iuc
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2 # module at all by setting the value below to 1 for the
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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3 # modules you want to remove.
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7b0207bd2183 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2f544e337886709995a93d53f394919ce8e4673a
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4 duplication ignore 1
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5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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5 kmer ignore 0
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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6 n_content ignore 0
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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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
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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10 gc_sequence ignore 0
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7b0207bd2183 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2f544e337886709995a93d53f394919ce8e4673a
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11 quality_sequence ignore 1
7b0207bd2183 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2f544e337886709995a93d53f394919ce8e4673a
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12 tile ignore 1
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5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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13 sequence_length ignore 0
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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14 adapter ignore 0
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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16 # For the duplication module the value is the percentage
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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17 # remaining after deduplication. Measured levels below
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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18 # these limits trigger the warning / error.
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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19 duplication warn 70
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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20 duplication error 50
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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22 # For the kmer module the filter is on the -log10 binomial
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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23 # pvalue for the most significant Kmer, so 5 would be
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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24 # 10^-5 = p<0.00001
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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25 kmer warn 2
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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26 kmer error 5
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5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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28 # For the N module the filter is on the percentage of Ns
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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29 # at any position in the library
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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30 n_content warn 5
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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31 n_content error 20
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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33 # For the overrepresented seqs the warn value sets the
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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34 # threshold for the overrepresented sequences to be reported
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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35 # at all as the proportion of the library which must be seen
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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36 # as a single sequence
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7b0207bd2183 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 2f544e337886709995a93d53f394919ce8e4673a
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37 overrepresented warn 0.001
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38 overrepresented error 1
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40 # The per base quality filter uses two values, one for the value
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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41 # of the lower quartile, and the other for the value of the
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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42 # median quality. Failing either of these will trigger the alert
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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43 quality_base_lower warn 10
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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44 quality_base_lower error 5
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45 quality_base_median warn 50
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46 quality_base_median error 20
5b995cef2fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
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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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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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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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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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80 adapter warn 5
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81 adapter error 10
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83
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