How does one interpret the output from a 'PGLS-Relationships' analysis in Compare 4.6b?

03 April 2015 3,286 0 View

For a PGLS analysis in Compare 4.6, can anyone propose sources of error or solutions for the following problems?

I am using Compare 4.6 software to perform PGLS on a large set of trait values using a known phylogeny (based on genetic distance; Taxa = 23, Traits = 110, phylogeny = 1). The problem is that when...

03 April 2015 845 1 View

RAPD PCR: does every sample require a technical replicate or will a subset suffice?

In the interests of conserving time and resources, I would like to avoid performing replicates on every single sample, unless this is absolutely necessary. I have read in the literature that 5-10%...

07 August 2014 6,800 4 View

What statistical methods can be used to determine reproducibility between more than two groups of replicate samples?

I am analysing data obtained from experiments conducted on a group of 10 individuals in triplicate. In each replicate, the number of data points are not necessarily the same for each of the...

11 December 2013 2,693 4 View

Can you re-position a DNA ladder in a gel picture (you plan to publish) using image editing methods?

I am thinking about publishing work based on RAPD PCR. The problem I am having is that my gel pictures consist of several different experiments/primers (represented by 10 samples each) beside a...

07 August 2013 5,266 5 View

Can anyone provide an example of an input file for the program DfDist (Beaumont, 2008)?

The program detects loci influenced by selection by comparing their Fst values to a neutral simulation.

08 September 2012 3,055 2 View

Could anyone give an example of AFLP presence/absence data written in Genepop format?

I have seen examples of the Genepop format, but never for dominant markers. Could anyone, additionally, provide a clear explanation of the format's characteristics?

08 September 2012 7,811 0 View

In what format should AFLP data be submitted to software used for detecting selection?

I am aware that the detection is based on Fst values. However, should these be obtained using another program and then be transferred to DfDist, Bayescan etc. or should AFLP binary data be used...

08 September 2012 3,245 0 View

In preliminary screening of AFLP primer combinations to determine pairs which give optimal results, how many individuals should be screened?

Is this randomly decided by the researcher or is there a general principle they can base their decision on? I have read many papers looking for an answer but have yet to find an explanation on...

07 August 2012 3,348 7 View

How do I increase the yield of my PCR product?

Hello, We would like to increase the yield of our PCR product. We are running a series of PCR reactions that is targeting ~1.1kb sequence. We begin each reaction with ~400pg of template DNA...

02 March 2021 4,029 3 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

How to address this issue in the analysis of Real-Time PCR results?

To dear Researchers, I was analyzing a series of concentration for estimation of Real-Time PCR efficiency. The concentration was 1:10. I used MS-excel to evaluate Slope. The result of slope was -8...

01 March 2021 8,683 4 View

No title

Does anyone have the experience of using Taq Man probes in the QIAGEN Rotar- Gene qPCR machine?

01 March 2021 5,311 1 View

MiRNA qpcr problem?

Dear All, mirna primer showing some problem in the melting curve? any idea why? As attached is the melting curve. The forward sequence is obtained from miRBase and reverse primer is universal.

28 February 2021 5,008 4 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Can thermal cycler machines be problematic during PCR?

Hi, my question is about the heating of thermal cycler machines and I hope some of you had experienced a similar thing previously. There are two thermal cycler machines in the lab(BioRad) and for...

26 February 2021 4,777 4 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Why do the PCR bands from the cDNA templates (extraction from the cell after transfection) show different size from the band of the plasmid template?

After transfection with the plasmid ( linearized ) and subcloning of the cell lines, RNA was extracted from the cell and then reverse transcripted to cDNA. When PCR reactions were run to verify...

25 February 2021 5,712 3 View