Can someone advise on using qiime?

More Niti Jadeja's questions See All

What will be best bacterial genome alignment tool for comparative analysis in terms of single nucleotide variation due to stress ?

Bioinformatic tool for genome variation comparision.

04 May 2018 1,088 1 View

Which is the primer designing tool recommended for gene expression studies?

Critical factors like codon, start codon, re site incorporation, etc have to be dealt with in making primers for gene expression studies, and hence: are there any recommended Softwares for the...

31 December 2013 8,190 13 View

Can anyone recommend a good vector for cloning a PCR amplified catabolic gene for protein expression studies?

I am trying to clone a catabolic gene amplified from metagenome via precise primer design.

09 October 2013 2,045 13 View

Track the difference

I have 2 bacterial genome sequences- i.e draft genomes. The genus are the same, but to discriminate on species level, what tools can I apply? There are a set of genes similar in both strains and...

11 December 2012 934 10 View

Has anyone used CopyControl Fosmid Library Production Kit? What are the product reviews?

I would want to use it for metagenomic library production.

08 September 2012 6,236 0 View

Anyone using Copy Control Bac cloning kit for metagenomic library construction?

Sludge metagenomic Library

08 September 2012 2,165 0 View

Is anyone dealing with Metagenomic library construction from sludge DNA ?

I am to begin one such task and have decided on Bac as my cloning vehicle, and restriction digestion as the next step using BamH1 and pst1.

04 May 2012 6,359 5 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

I'm optimizing a tetra-ARMS PCR protocol with amplicon sizes: 165bp, 123bp and 93bp. Why, in the gel, only 165bp is visible while I'm expecting all 3?

It's an end-point PCR protocol. I'm using 1.5% agarose gel with SyBR Safe dye and TBE as a running buffer, visualization on BioRad XR+ system. I was primarily thinking of primer efficiency,...

01 August 2024 4,673 4 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 View

How to retain amplicon yield after Ampure bead cleanup, following a 2-stage PCR protocol?

Hello all, I have been trying to follow a 2-stage PCR protocol used to amplify barcodes of a large yeast library, as per Nyugen et al. (2022) -...

30 July 2024 841 2 View

Why running a restart analysis in Abaqus in Ubuntu OS gives an error as attached when running the same job in Windows doesn't give any error and runs?

I am trying to run a restart analysis, which imports deformed configurations of parts from a generated ODB file. It runs fine in Windows OS but when I try to run it in Linux OS, it is giving some...

29 July 2024 9,572 3 View

Could you try using PeptiCloud and see if it's a useful tool for biology research?

PeptiCloud (www.pepticloud.com) is a bioinformatic platform that allows researchers to organize and share their data for their projects as well as collaborate with others in one place. Through...

28 July 2024 4,762 2 View

Should the amount of DNA input used for ChIP-seq library preparation be matched between the control and experimental groups?

Hi all. As a beginner in ChIP-seq experiments, I hope you understand that the following questions might be somewhat basic. I am planning to perform ChIP-seq or MeDIP-seq analysis to investigate...

28 July 2024 6,938 1 View

Are there always been barcodes, apapters and primer sequences in the FASTQ files of NGS?

Hello researchers, Sorry for my stupid question. I am learning the QIIME2 workflow for analyzing some 16s amplicon NGS fastq data. I found a very nice paper with data and code public available...

20 July 2024 5,405 2 View

Printing residues in an object in Pymol?

Hi! I am currently working on a protein where I have selected residues within 10A of its bound ligand in pymol. However, I can not find a way to print out what residues are contained in that group...

15 July 2024 1,727 1 View

Looking for a bioinformatics expert especially one who has expertise in Nanoparticles docking ?

Silver Nanoparticles docking with alpha amylase and alpha glusidase .

11 July 2024 6,883 2 View

Alexander J. Probst

Check this:

https://groups.google.com/forum/#!forum/qiime-forum

Best, Alex

Niti Jadeja

thanks Alexander .......

Erik Dassi

The overview tutorial on QIIME website is very nice and guides you through all steps of the analysis...have a look here: qiime.org/tutorials/tutorial.html

Thanks a lot Alida ........!