Rakeshkumar Yadav

11 Questions 23 Answers 0 Followers

Questions related from Rakeshkumar Yadav

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...

11 November 2019 2,421 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...

08 August 2019 4,037 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....

04 April 2019 7,206 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...

10 October 2018 7,757 0 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...

09 September 2018 5,396 1 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...

09 September 2018 3,285 4 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...

09 September 2018 6,385 15 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...

12 December 2017 7,882 4 View

Can anyone explain what is meant by water memory and is there any role of electromagnetic waves in it?

04 April 2017 3,815 0 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?

12 December 2016 6,916 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 4,488 0 View