Which parameter sets are optimal for stack assembly?

More Ngoc Nguyen's questions See All

Why are my bands weird in this Agarose gel?

Can someone please give me some possible things that could go wrong? Here is my recipe: 0.5g Agarose 50 mL of TAE 1x 1 uL ethyl bromide. Gel was run at 100V for 1 hour. The buffer used is also TAE.

01 March 2021 9,952 3 View

How to increase solubility of Poly acrylic acid in Dioxane solvent?

I am working with Polyacrylic acid (100.000Da) and instead of water, I need to use another solvent (dioxane) to dissolve PAA. However, because of the high molecular weight, it's quite hard to...

25 February 2021 2,225 5 View

How to minimise the risk of being abused the profile of potential participants tagged in a social media post?

Dear colleagues, I got this one in one project I did ethics review. It's great to hear about your thoughts/experiences. "Doing an open recruitment online (i.e., via Facebook) requires public...

22 February 2021 3,322 3 View

Any suggestion on self-efficacy scale ?

Dear researchers, I am planning on conducting a research on the relationship between Language learning strategies, by Oxford (1990) and self-efficacy. I have found Morgan-Jinks Student Efficacy...

22 January 2021 8,432 3 View

I need to apply a questionnaire from an article. What statistical analysis do I need to use?

Hello, I found a survey about attitude toward language in an article which I find fit to use it in my thesis. The survey has 30 questions, which were put into 5 factors through factor analysis...

21 January 2021 9,419 3 View

The sufficient EMG sensing electrodes layout in studying occlusionology?

Hi all researchers, I would like to have your practical experience in EMG-based occlusional examnation with the relevant existed commercialized systems of Gamma Dental, SAM, and the others. If...

20 January 2021 1,757 1 View

Why did I obtain abnormal staining by TUNEL assay?

I use Abcam TUNEL Assay Kit - HRP-DAB (ab206386) on mouse tissues. The staining showed a pattern that I expected to see with a specific layer of cells dying due to drug treatment. But the...

12 January 2021 144 1 View

Is there a generalized method to derive current-mode model of any DC-DC converters?

Hi all, As new DC-DC converters are being proposed, associated control method should be proposed and based on the small-model signal analysis of the DC-DC converters. Using average space state...

06 January 2021 7,247 3 View

Is it need to test Cronbach's Alpha for extracted features from data?

As Cronbach's Alpha is usually used for test the reliability of measurements given by questionnaires, however, I wonder that whether I use this test for features extracted from behavioral data. I...

26 December 2020 9,602 2 View

How is datasets good?

Can you show me some ways to generate benchmark datasets?

22 December 2020 362 4 View

Can we classify HV and LV lines based on line length?

I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...

03 March 2021 4,116 4 View

What analysis to choose with a large neste dataset and clearly skewed or kurtotic distributions?

Hello! I have a dataset of n=3000 nested within 8 countries with approximately 200 or 400 responses in each country. I originally planned to perform multilevel modelling with 4 dependent variables...

02 March 2021 6,865 1 View

Do you know any MR image dataset?

I would like to research on MR images (0.5T and 3T). Can you please suggest some websites that I can download dataset including both 0.5T and 3T MR images? Thank you.

02 March 2021 7,735 3 View

Can NFL theorem be valid in infinite search space in ML?

NFL theorem is valid for algorithms training in fixed training set. However, the general characteristic of algorithms in expanded or open dataset has not been proved yet. Could you show your...

01 March 2021 1,189 3 View

Does anyone have kinetic and kinematic dataset for gait classification?

I want to differentiate between normal and abnormal movement. For this reason, I am looking forward to this type of dataset.

01 March 2021 9,485 1 View

Where can I find public datasets with Covid-19 patient information?

Hi, I'm looking for public datasets that have CT, X-ray information, or medical records for patients with Covid-19. Does anyone have suggestions?

28 February 2021 4,760 3 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

I need dataset for recommandation system?

Hi every body I need to collect datasets from different source to work on recommendation system algorithms, could you advise me how collect data?

27 February 2021 7,063 7 View

How to evaluate unsupervised clustering metrics when some elements do not have a cluster label in the result?

I run algorithms like HDBSCAN and MeanShift, and compare them with K-means and GaussianMixture. The first two algorithms do not return cluster labels for some elements in the dataset. My question...

27 February 2021 428 3 View

How to download dataset?

I have to download dataset from software infrastructure repository (SIR) and I have created account on repository but I am not able to download plz guide.

25 February 2021 3,840 2 View

Jose Alberto Lopez-Aleman

I believe this papers may be helpful for you:

Article Lost in parameter space: A road map for Stacks

Article Restriction site-associated DNA sequencing, genotyping error...

My personal recommendation (which is used in various researches) is to take a subset of your samples (one that covers a broad range of your data) and follow the Paris et al. method (from the first paper).

Ngoc Nguyen

Jose Alberto Lopez-Aleman Thanks for your answer, the paper really helpful!

Ginushika Premarathne

Hi,

In denovo_map.pl the M, n, and m parameters are critical. You can check the suitable parameter set by running the analysis number of times while changing the parameters. Then using a PCA diagram or Cluster dendrogram you can confirm the suitable parameter set for your data. In most cases, optimal parameters are M 4, n 4, m 3. Then when you are running populations program R, r, p is important.