Bridge PCR

A bridge fragment form or “colony DNA” and solid surfaces are PCR amplified using primers to link the “DNA cluster.” Method, another method for in vitro clonal amplification, Illumina Genome Analyzer sequencer in it is used. Single molecular method to that developed by (sold by after Helicos) laboratory Steven quake such is an exception: event based on the DNA molecules of the individual eliminates them of the need, attached to the surface In order to detect, using molecular amplification bright laser excitation and fluorophore. Duplicate PCR is a discomfort of everyday in the sequence. To spend hundreds or thousands of dollars to end the sequencing, When you get the lead back once, you can see that a few percent, you is a copy of the same to each other 70% of your leads 30% sometimes . Is called a PCR overlap, they are recommended (MarkDuplicates the available tools of two samtools rmdup 2 and Picard) mark, them or at least removed sequencing pipeline most.

It, what it means to read to replicate the PCR, why ignore them – since you walk in order, I wanted to know how to duplicate these occur? Never again and again to search Google for it, you have found an adequate description of me. So, after hearing that was held to introduce the excellent technology of sequence and biochemistry on the first day of the course, overlap of the PCR, the way he that occur in the next generation sequencing I UAB sequencing Shawn Levy asked. I will explain the response he gave me in this article. Duplicate PCR occurs in step 3. In Step 3, as to have them of enough for the amount of PCR overlap any, it is inevitable that intentionally have multiple copies of the genomic DNA of the original molecule, respectively. When duplicate PCR occurs, the two copies of the original molecule a single grass primers on different intracellular beads and various. Ideally, in Step 3, because (said Shawn Levy and prefer not to 6 round, 26 more than the absence of PCR he therefore) 64 times to just you, the library “Complexity” is still high, information entropy to increase ie. This will allow you are reading that then might be as low as 4% overlap PCR some of your last. If the starting material, or because the difference of fragment size very large people rate of overlapping PCR is high, for example, people of 30% as required in step 3 is a large amplification of the library a little, the smaller the The presentation of the developmentally finally when you have, fragment easy to amplify the PCR.

All this, I depend on the description, and random distribution of the molecules of the beads of molecules that have been performed in step 4. If you have a cluster or monoclonal beads of time get to step 5, you only will be able to interpret the generated reading. Polyclonal beads – DNA molecules of different, when you arrive in Step 4 – occurred in the sequence always, the software sequencer, you should be ignored by suppressing those clusters or picotiter well those in the production cell. Similarly, DNA molecule does not suspend, here, the software will ignore the empty cluster or dry hole. Because sometimes, and hybridized to the grain of any other (for example, 2 out of 64 copies made per molecule) to multiple copies of, to load the same DNA and within the well / cluster two different molecules of the same original – PCR own duplicate them. However, as with the DNA molecule unique and some one DNA molecule exactly, of DNA, purpose the concentration of the lawn in step 4 Beading / accurate for the most part most likely of beads / cluster It is to have but one degree more than is presented.

Does that make sense? I sat down, you had to work through the possibility itself. Random hybridization of DNA molecules of the beads, is complex: After drawing a ball of color from other cells, would be like dropping a ball of them in a separate container to it. Read N times the results … assuming assumption of simplification, the DNA molecule, as is the question of how to represent a 0, 1, 2 finally all beads and only monoclonal end. Poisson model is a simplified import here (K = 0) against the sky polyclonal beads and pearls “select” of the DNA molecule (K> = 2) monoclonal against (K = 1) is made to take into account the choices of other does not. Shawn Levy, 50-80% of the wells ion Trent sequence and Roche, said that means that as a Poisson distribution, this process can be modeled, it is occupied by the monoclonal ball. The lambda value not receive 1 / above, and figure 37% = 1 of the probability density for F = ~ k that you can see that it does not exist, about 50 ~ of the probability density, which means if you play with the Poisson distribution you there 80%. Probably is related to the water / oil emulsion – it, I suppose monoclonal increases, chemical magic of some that there is going on here.

I have been talking almost exclusively in terms of pearl is the job of ion Trent bedding how Roche 454. I do not know much about how Illumina technology is divided into separate groups, to get the molecule, but also the model above, I assume that you have the relevance of some of the technology are.  As if it had the beads twice the molecule unique, if you try to use it in data library very low, you will decompose this model. Poisson distribution, is the probability that a unique copy of the molecule unique to read that you give us here really. It is used for PCR overlaying rate range, it is possible to obtain a meaningless answer mean that it has failed in (> ~ 1) higher lambda acquires unique unique you read than your Low lamdba, molecules can be.  I, considering how good the amplification bias of the model, it does not appear How you influence the overlapping courses there are many still here, but, and I do not fully understand. Intentionally we, to make a copy of many of the molecules of each, but why they are this simple model that leads the complexity of the library (in preparation for a good library) was limited because it is rare to large more, in order to understand why the duplication of the PCR occurs, it is really useful to me. I will replicate the price. So that there is the amplification bias, is the moral of the story for those who do the preparation of the library, since the DNA was extracted as a starting material, to get the molecule more unique than is possible in the ultrasound machine, Minimization try to get the tight distribution of fragment size.