Excellent, Thank you very much. This answers my non-bioinformatics question
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27atcggcta27
What stops clusters from merging during bridge amplification?
Hello Everyone!
I'm sorry if this is answered somewhere else, If it is please direct me to it. I cant seem to find much information.
I'm wondering how DNA fragment clusters dont get all mushed together on a flow cell when sequencing after bridge amplification.
It is my understanding that during RNA-Seq, RNA is converted to DNA, then the DNA is fragmented. The resulting fragments are layed out on a flow cell, amplified by bridge amplification to get stronger light detection, and then sequenced.
So my confusion stems from this thought: If DNA fragments are dispersed randomly throughout a flow cell, and then amplified by bridge amplification, what is preventing the clusters from merging? I made a picture (see link below) to better describe my question.
Pictorial depiction of my confusion
I guess my question could also be reworded as "What prevents DNA fragments from amplifying too close to each other in a flow cell?"
Thank you in advance!
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1 answer
This is not a bioinformatics question but briefly
What prevents DNA fragments from amplifying too close to each other in a flow cell?
For a patterned flowcell, the physical presence of a nano-well, which is a defined physical well.
For non-patterned flow cells nothing prevents that. Clusters can indeed touch or merge/mix. "Chastity filtering" included in bcl2fastq pre-processing detects and removes any clusters that fail this cluster purity filter.
Accurate quantitation of libraries and appropriate loading concentrations are keys to minimizing this problem.
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Hello 27atcggcta27!
We believe that this post does not fit the main topic of this site.
Answered by Genomax in reply
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