Difference between overrepresented and duplicated sequences
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The analysis of overrepresented sequences will spot an increase in any exactly duplicated sequences, but there are a different subset of problems where it will not work.
If you have very long sequences with poor sequence quality then random sequencing errors will dramatically reduce the counts for exactly duplicated sequences.
If you have a partial sequence which is appearing at a variety of places within your sequence then this won't be seen either by the per base content plot or the duplicate sequence analysis.
The Kmer module starts from the assumption that any small fragment of sequence should not have a positional bias in its apearance within a diverse library. There may be biological reasons why certain Kmers are enriched or depleted overall, but these biases should affect all positions within a sequence equally. This module therefore measures the number of each 7-mer at each position in your library and then uses a binomial test to look for significant deviations from an even coverage at all positions. Any Kmers with positionally biased enrichment are reported. The top 6 most biased Kmer are additionally plotted to show their distribution."
If you have very long sequences with poor sequence quality then random sequencing errors will dramatically reduce the counts for exactly duplicated sequences.
If you have a partial sequence which is appearing at a variety of places within your sequence then this won't be seen either by the per base content plot or the duplicate sequence analysis.
The Kmer module starts from the assumption that any small fragment of sequence should not have a positional bias in its apearance within a diverse library. There may be biological reasons why certain Kmers are enriched or depleted overall, but these biases should affect all positions within a sequence equally. This module therefore measures the number of each 7-mer at each position in your library and then uses a binomial test to look for significant deviations from an even coverage at all positions. Any Kmers with positionally biased enrichment are reported. The top 6 most biased Kmer are additionally plotted to show their distribution."
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