Hello,
I was recently discussing Illumina FASTQ files with someone and the following question came up:
Why do some Ns have higher quality values than other Ns? Shouldn't they all be the same?
As I understand it, an N pops up when the intensity between 2 bases is so close that the base caller decides that it cannot decide which base was sequenced.
As for higher quality Ns, another part of the base calling depends on how isolated the cluster is. I guess that a higher quality N means that the cluster was more isolated (at least non-overlapping with others) than an N with a low quality. If the cluster is more isolated then the intensity readings should be higher, right?
Just as a cultural fact, we would like to know the correct answer ^_^
Greetings,
Leonardo
I was recently discussing Illumina FASTQ files with someone and the following question came up:
Why do some Ns have higher quality values than other Ns? Shouldn't they all be the same?
As I understand it, an N pops up when the intensity between 2 bases is so close that the base caller decides that it cannot decide which base was sequenced.
As for higher quality Ns, another part of the base calling depends on how isolated the cluster is. I guess that a higher quality N means that the cluster was more isolated (at least non-overlapping with others) than an N with a low quality. If the cluster is more isolated then the intensity readings should be higher, right?
Just as a cultural fact, we would like to know the correct answer ^_^
Greetings,
Leonardo
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