Questions tagged [pcr]
The pcr tag has no usage guidance.
12
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1.What size PCR product will be generated using the primers (bold and underlined) in the sequence below?
I would like to know the steps of this question and how to determine the forward and the reverse primers and also the length of the sequence, without using NCBI. If you could explain and give an ...
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Do we design primers for single stranded DNA with same criteria as we do for double stranded DNA?
I am trying to design primers for a single stranded DNA virus.
But I am having a dilemma as whether we design the primers same way as double stranded DNA?
do we have to design forward and reverse ...
- 113
1
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69
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Choosing the best number of species for assay
I am doing amplicon sequencing of a virus across many different regions. Lets say I have 20k unique variants of the same virus that I put into my pcr assay and after sequencing and amplifications I am ...
- 121
3
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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 ...
- 1,427
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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........... ...
- 11
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3
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134
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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 ...
1
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1
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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 ...
- 123
3
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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 ...
- 131
1
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174
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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 ...
- 1,783
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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".
...
- 241
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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 ...
- 3,141
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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 ...
- 3,141