I have noticed that in our MiSeq runs we seems to always have an abrupt change in base composition in the last one or two cycles. The proportion of A goes to zero. Also I noticed we have a cyclic pattern in base proportions in the rest of the cycles, except the first 10 or so where there seems to be some other bias going on.
On the other hand, the data from a HiSeq X run shows no such cyclic variation, nor the sudden drop in As at the end.
See this image for base composition comparisons
Does anyone have an idea of what is causing these patterns in the MiSeq, and why they are not seen in the HiSeq run?
Note that these were two different libraries from different organisms. Both were TruSeq DNA PCR-free with Covaris ultrasonic shearing.
Jon
On the other hand, the data from a HiSeq X run shows no such cyclic variation, nor the sudden drop in As at the end.
See this image for base composition comparisons
Does anyone have an idea of what is causing these patterns in the MiSeq, and why they are not seen in the HiSeq run?
Note that these were two different libraries from different organisms. Both were TruSeq DNA PCR-free with Covaris ultrasonic shearing.
Jon
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