This is the PhiX lane--anyone seen bases diverge like this? What would cause this? Thanks
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Did you use all defaults for the solexa pipeline? Chastity filter of 0.6?
Mid way through the read, there comes a point where A and C, G and T become quite dependent on each other, and the pipeline uses all kinds of matrices to call one from the other.
What is the dna sample, if I may ask!--
bioinfosm
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Did you use all defaults for the solexa pipeline? Chastity filter of 0.6?
Mid way through the read, there comes a point where A and C, G and T become quite dependent on each other, and the pipeline uses all kinds of matrices to call one from the other.
What is the dna sample, if I may ask!
Huh?
The only corrections the Solexa pipeline performs are crosstalk and phasing corrections. Crosstalk is determined from the first cycle only, and the same matrix is applied to all cycles. The Phasing correction is cycle dependent but is unlikely to cause anything like this.
Would need to see more plots (all intensities/called intensities) in order to figure out what's happening in this case.
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