correlation in per base sequence quality profiles of multiplexed samples.
I have a question related to the "per base sequence quality" profiles.
In a Illumina HiSeq 150bp paired end runs of multiplexed samples, I found that the "per base mean sequence quality" profiles of all the samples correlate with each other. Please see the attached file for figures of quality profiles of all samples, for forward(read1) and reverse (read2) reads.
Though the variation in quality is very small (within 1 quality score), I was expecting that the variation should be rather random for each sample. Is this normal and a common occurrence, and a characteristic of the machine, with something to do with the base calling at each cycle?
* There is a prominent dip in quality at around 105 position in both forward and reverse reads. I was advised by the Sequencing provider that this is a common occurrence, associated with an increase in the laser intensity which occurs around this position. Is it true for all HiSeq runs?
Thanks for your suggestions.
In a Illumina HiSeq 150bp paired end runs of multiplexed samples, I found that the "per base mean sequence quality" profiles of all the samples correlate with each other. Please see the attached file for figures of quality profiles of all samples, for forward(read1) and reverse (read2) reads.
Though the variation in quality is very small (within 1 quality score), I was expecting that the variation should be rather random for each sample. Is this normal and a common occurrence, and a characteristic of the machine, with something to do with the base calling at each cycle?
* There is a prominent dip in quality at around 105 position in both forward and reverse reads. I was advised by the Sequencing provider that this is a common occurrence, associated with an increase in the laser intensity which occurs around this position. Is it true for all HiSeq runs?
Thanks for your suggestions.
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