How do I decide the parameters to run diamond aligner?

My goal is to align my metagenomic sequences with virulence gene database in order to find out which probable genes are prevalent in the data. So I ran diamond aligner using following...

10 November 2019 2,333 2 View

Do i need to do betadispersion after Adonis test?

I am analyzing a meta genomic data and I want to comment about the significance of beta diversity for the samples taken from different locations. In order to do that i did Adonis test (seed of...

07 August 2019 3,969 4 View

Please suggest any bioinformatic tools or lab-based experiments to validate the metagenomic data?

I am looking to validate the information generated from metagenomic sequencing. I know that I can carry out qPCR to validate my data. And I guess Random forest regression analysis can be done too....

03 April 2019 7,128 1 View

Can I convert Nanopore data reads Fast5 or fastq format in to biom format and proceed with the analysis using R ?

Previously, I have done illumina data analysis so have experience in doing that. However, Nanopore is bit new to me and I am quite confused in its data analysis. I have epi2me (I guess it uses...

09 October 2018 7,669 0 View

Wondering how to enrich or concentrate phages or viruses for community phage/virus nucleic acid extraction and that too without using host?

We all know about the specificity of viruses or phages and I guess that would specially limit their enrichment to certain groups. Suppose I have a sediment or sewage sample and I want to enrich...

08 September 2018 6,274 15 View

Validation of NGS taxa abundance data? or any other method (experimental or bioinoformatic based) to validate NGS results?

Hello, I have been looking out for studies which have actually tried to validate the results from NGS data. One technique I know is Real Time-PCR. I was actually looking out for real time PCR...

08 September 2018 3,203 4 View

Can any one explain Mantel Test in simple terms ?

I am trying to understand mantel test in terms of getting to a biological conclusion. I referred few papers but failed to understand it completely. I have understood that it is a correlation...

08 September 2018 5,326 1 View

Can anyone suggest me modification/s or method of DNA extraction from sediments of estuary?

I have been trying to extract DNA with no success. I have used following methods 1. PCI method with and without bead beating 2. kit methods qiagen, himedia 3. interchange of reagents 4. cold and...

11 December 2017 7,805 4 View

How one can predict the metabolic pathway using bioinformatic tools( if any) for a novel compound, if the structure of compound is known ?

source organism is also known. nearest match for structure with 80% similarity is found. is it possible?

11 December 2016 6,855 3 View

Significance of PCoA plot using PERM ANOVA

Recently, I read an article on AMF succession. In order to explain the dissimilarity in AMF Counts, they have used PCoA plot. Mostly , I have seen the PCoA plot are being constructed by using...

01 January 1970 4,395 0 View

How do I determine the degree of polymerization of PEG 400 based on NMR integration?

Hello, I am working on the photocatalytic degradation of PEG 400. I would like to know if it's possible to determine the degree on polymerization based on NMR integration, or by the MW of the...

02 March 2021 6,186 3 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

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View

How to compute the internal consistency of a scale with ordinal items?

Hi community, I am trying to determine what is the best way to calculate the internal consistency of a newly developed self-esteem scale. I am working together with two other researchers on the...

28 February 2021 1,369 5 View

What could be some reasons why unstimulated monocytes are getting activated?

Im doing PBMC isolation -> CD14+ enrichment using magnetic beads -> stimulation setup. My negative control is just cells in cRPMI but they seem to get activated over and over again.

28 February 2021 7,883 3 View

What is Flat Lens Antenna?

28 February 2021 5,433 3 View

How to include original NMR data in a manuscript?

hello. i am junior researcher. I received a comment from a reviewer that he could not find NMR data in my submitted paper. I had included the NMR graph with explanation and formula to calculate...

27 February 2021 734 4 View

Can impedance of antenna be less than 50 ohms?

I am simulating helix antenna in hfss, right now, giving excitation with 50 ohms port. When I see the results of Z parameter (real). It shows lower than 50 ohms. Do not understand, if it can be...

27 February 2021 4,218 7 View

How can I set up a good fit SEM model in AMOS?

I am trying to make an SEM model in AMOS for my dissertation but having some trouble with getting a good fit. I am looking for relationships between self-efficacy reported on a Likert scale and...

26 February 2021 8,642 4 View

Inpatient DBT to reduce parasuicidal behaviour?

Currently trying to obtain as many pieces of research as possible for my dissertation around the implementation of DBT within the inpatient unit for those with a diagnosis of BPD. Primarily...

23 February 2021 5,654 2 View