I would like to know how illumina platform like MiSeq or NextSeq knows which reads are from PhiX and which from the sequencing DNA? How is this differentiated at the beginning of sequencing?
Thank you for ideas :)
The platform itself doesn't know which reads are PhiX, you (or the sequencing company) need to remove the PhiX reads during quality filtering.
Thank you, José.
We always do that, but I thought it was an internal control of the proper sequencing that works from the beginning... It's not like that?
I don't know. I mean, it is a control for the quality of the running, but I don't know how it exactly works...
Sorry for not clarify your dudes.
After sequencing, during demultiplexing (separating reads into distinct fastq files based on sample indices you used when amplifying libraries) you'll lose anything from phiX (since it won't have any index you used).
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