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We have observed a couple of relatively frequent (1:4) SNPs in what is supposed to be a clonal culture. The simplest explanation is that it's not a clonal culture, but has anyone ever observed what seem to be non-random sequencing errors on an Illumina platform? In other words, context-dependent errors?
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Yes...
What platform/chemistry are you using? Also, have you tried this? It should greatly reduce the quality scores of bases that are involved with some sort of nonrandom error-inducing motif. -
It might also be interesting to report the problematic sequences, given that specific sequences are know to give non random errors.
For example, sequencing errors have been report with inverted repeats and GGC sequences on some Illumina platforms.Comment
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