Mercurial > repos > devteam > fastqc
comparison test-data/fastqc_customlimits.txt @ 1:8fae48caaf06 draft
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| author | devteam |
|---|---|
| date | Tue, 11 Nov 2014 12:46:27 -0500 |
| parents | |
| children | a00a6402d09a |
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| 0:e28c965eeed4 | 1:8fae48caaf06 |
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| 1 # For each of the modules you can choose to not run that | |
| 2 # module at all by setting the value below to 1 for the | |
| 3 # modules you want to remove. | |
| 4 duplication ignore 1 | |
| 5 kmer ignore 0 | |
| 6 n_content ignore 0 | |
| 7 overrepresented ignore 0 | |
| 8 quality_base ignore 0 | |
| 9 sequence ignore 0 | |
| 10 gc_sequence ignore 0 | |
| 11 quality_sequence ignore 1 | |
| 12 tile ignore 1 | |
| 13 sequence_length ignore 0 | |
| 14 adapter ignore 0 | |
| 15 | |
| 16 # For the duplication module the value is the percentage | |
| 17 # remaining after deduplication. Measured levels below | |
| 18 # these limits trigger the warning / error. | |
| 19 duplication warn 70 | |
| 20 duplication error 50 | |
| 21 | |
| 22 # For the kmer module the filter is on the -log10 binomial | |
| 23 # pvalue for the most significant Kmer, so 5 would be | |
| 24 # 10^-5 = p<0.00001 | |
| 25 kmer warn 2 | |
| 26 kmer error 5 | |
| 27 | |
| 28 # For the N module the filter is on the percentage of Ns | |
| 29 # at any position in the library | |
| 30 n_content warn 5 | |
| 31 n_content error 20 | |
| 32 | |
| 33 # For the overrepresented seqs the warn value sets the | |
| 34 # threshold for the overrepresented sequences to be reported | |
| 35 # at all as the proportion of the library which must be seen | |
| 36 # as a single sequence | |
| 37 overrepresented warn 0.001 | |
| 38 overrepresented error 1 | |
| 39 | |
| 40 # The per base quality filter uses two values, one for the value | |
| 41 # of the lower quartile, and the other for the value of the | |
| 42 # median quality. Failing either of these will trigger the alert | |
| 43 quality_base_lower warn 10 | |
| 44 quality_base_lower error 5 | |
| 45 quality_base_median warn 50 | |
| 46 quality_base_median error 20 | |
| 47 | |
| 48 # The per base sequence content module tests the maximum deviation | |
| 49 # between A and T or C and G | |
| 50 sequence warn 2 | |
| 51 sequence error 5 | |
| 52 | |
| 53 # The per sequence GC content tests the maximum deviation between | |
| 54 # the theoretical distribution and the real distribution | |
| 55 gc_sequence warn 15 | |
| 56 gc_sequence error 30 | |
| 57 | |
| 58 # The per sequence quality module tests the phred score which is | |
| 59 # most frequently observed | |
| 60 quality_sequence warn 27 | |
| 61 quality_sequence error 20 | |
| 62 | |
| 63 # The per tile module tests the maximum phred score loss between | |
| 64 # and individual tile and the average for that base across all tiles | |
| 65 tile warn 5 | |
| 66 tile error 10 | |
| 67 | |
| 68 # The sequence length module tests are binary, so the values here | |
| 69 # simply turn them on or off. The actual tests warn if you have | |
| 70 # sequences of different length, and error if you have sequences | |
| 71 # of zero length. | |
| 72 | |
| 73 sequence_length warn 1 | |
| 74 sequence_length error 1 | |
| 75 | |
| 76 # The adapter module's warnings and errors are based on the | |
| 77 # percentage of reads in the library which have been observed | |
| 78 # to contain an adapter associated Kmer at any point | |
| 79 | |
| 80 adapter warn 5 | |
| 81 adapter error 10 | |
| 82 | |
| 83 | |
| 84 |