Mercurial > repos > devteam > fastqc
view test-data/fastqc_customlimits.txt @ 3:0b201de108b9 draft
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author | devteam |
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date | Fri, 12 Dec 2014 10:55:57 -0500 |
parents | 8fae48caaf06 |
children | a00a6402d09a |
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# For each of the modules you can choose to not run that # module at all by setting the value below to 1 for the # modules you want to remove. duplication ignore 1 kmer ignore 0 n_content ignore 0 overrepresented ignore 0 quality_base ignore 0 sequence ignore 0 gc_sequence ignore 0 quality_sequence ignore 1 tile ignore 1 sequence_length ignore 0 adapter ignore 0 # For the duplication module the value is the percentage # remaining after deduplication. Measured levels below # these limits trigger the warning / error. duplication warn 70 duplication error 50 # For the kmer module the filter is on the -log10 binomial # pvalue for the most significant Kmer, so 5 would be # 10^-5 = p<0.00001 kmer warn 2 kmer error 5 # For the N module the filter is on the percentage of Ns # at any position in the library n_content warn 5 n_content error 20 # For the overrepresented seqs the warn value sets the # threshold for the overrepresented sequences to be reported # at all as the proportion of the library which must be seen # as a single sequence overrepresented warn 0.001 overrepresented error 1 # The per base quality filter uses two values, one for the value # of the lower quartile, and the other for the value of the # median quality. Failing either of these will trigger the alert quality_base_lower warn 10 quality_base_lower error 5 quality_base_median warn 50 quality_base_median error 20 # The per base sequence content module tests the maximum deviation # between A and T or C and G sequence warn 2 sequence error 5 # The per sequence GC content tests the maximum deviation between # the theoretical distribution and the real distribution gc_sequence warn 15 gc_sequence error 30 # The per sequence quality module tests the phred score which is # most frequently observed quality_sequence warn 27 quality_sequence error 20 # The per tile module tests the maximum phred score loss between # and individual tile and the average for that base across all tiles tile warn 5 tile error 10 # The sequence length module tests are binary, so the values here # simply turn them on or off. The actual tests warn if you have # sequences of different length, and error if you have sequences # of zero length. sequence_length warn 1 sequence_length error 1 # The adapter module's warnings and errors are based on the # percentage of reads in the library which have been observed # to contain an adapter associated Kmer at any point adapter warn 5 adapter error 10