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comparison test-data/fastqc_customlimits.txt @ 1:67355741fbc3 draft

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author devteam
date Tue, 11 Nov 2014 12:18:17 -0500
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0:d5e4121e45ed 1:67355741fbc3
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
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