Questions tagged [pcr]

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3 votes
1 answer
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How to optimize the number of amplicons ordered for a PCR wet experiment with several genomic ROIs?

Imagine we have an experiment for which we would like to minimize the number of purchased primers. Let's look at the layout of a single primer below: Assume we have a precomputed set of all necessary ...
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1 vote
1 answer
170 views

Need a alternative or more complex version of venn diagram in python for matching dna sequences

I am in google colab and I have combined and set up a data frame list of sequences that goes like this Location ID Sequence 1.1 ........ A ........ AAGAGATA 1.2 ........ A........... ...
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1 vote
3 answers
99 views

K means clustering, would PCA be a better option?

I have the data below. I need to use a clustering method to classify them and into categories of "Heterozygotote, Allele 1, Allele 2 and No Call. The values in RFU1 and RFU2 are used to determine the ...
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1 vote
1 answer
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In silico PCR: any models that can quantitatively predict the initial content from the end amplified result?

Let's say I've run the PCR and I now have a certain amount of the amplicon product. Is there any model that infers how much of it was there before the PCR started? I suspect it should be a ...
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3 votes
1 answer
271 views

Tool to remove a PCR contamination in NGS data

BACKGROUND I work on NGS data (illumina paired ends reads) coming from a full extract of RNA (metagenomic). We are interested in the viral fraction of this extract. I observed a contamination with a ...
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  • 131
1 vote
1 answer
126 views

How is PCR duplication rate computed in scATAC-seq?

Reading Cusanovich et al. (2015) I encountered the sentence: We mixed pairs of cell lines (HEK293T or HL-60 versus GM12878), performed combinatorial cellular indexing, and sequenced the resulting ...
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5 votes
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Correcting for noise in RT-qPCR gene expression data

I have a training set of RT-qPCR gene expression data (not run in triplicate) for a batch of samples with two phenotypes $A$ and $B$ on which I've trained a "logistic regression classifier". ...
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  • 249
5 votes
1 answer
3k views

Why do NEBNext indexing primers have sequence between the p5 oligo and index?

In a previous post I asked Why do NEB adapters have non-complementary sequence? Since then, I realized that there is some other sequence in the p5 indexing primer, as well as in the p7 indexing ...
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1 vote
2 answers
2k views

Why do NEB adapters have non-complementary sequence?

I am making some infographics of different library prep types and noticed something weird about NEB's Ultra II adapters. Molecule 1 is the desired product of the ...
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