Ahmad Ali

18 Questions 15 Answers 0 Followers

Questions related from Ahmad Ali

What are the suitable software to analyze the raw DNA sequences (meta-genomic data ) for microbial diversity analysis ?

what are the suitable software to analyze of raw DNA sequences for microbial diversity analysis ?

01 November 2018 4,159 3 View

How to avoid primer dimer formation ?? im getting primer dimer even after increasing the temperature, increasing DMSO , what should be done ??

how to avoid primer dimer formation ?? im getting primer dimer even after increasing the temperature, increasing DMSO , what should be done ??

19 February 2018 4,929 6 View

Can anyone help me in understanding and clearly interpreting ANOSIM (Analysis of Similarity) results given in a graph?

01 January 1970 7,153 1 View

How can I access the Phylogenetic diversity of a geographical region using 16s rRNA amplicon sequences?

I have a 16s rRNA amplicon sequences (next generation sequence), I want to find out the phylogenetic diversity of a geographical region, How can I do that? please tell me the different...

01 January 1970 6,435 4 View

What are the suitable software to analyze the 16S raw DNA sequences for microbial diversity analysis ?

What are the suitable software to analyze the raw DNA sequences (16S rRNA data ) for microbial diversity analysis ?

01 January 1970 7,232 6 View

What are the important data, parameters and software needed to predict a model the check the impact of climate change in a particular region?

what are the important data and parameters needed to predict a model to check the impact of climate change on a region? please suggest me your ideas to overcome this problem .

01 January 1970 9,133 4 View

Which bioinformatic tool is feasible to explain 16s metagenomic data ?

I have 16s metagenomic raw data to be analysed , please describe me different software and its work application to analyse it with respect to diversity ?

01 January 1970 1,155 2 View

Does anybody know how to extract Plasmid DNA from isolated genomic DNA.

I was working on plasmid isolation from an organism but i didn't got plasmid via plasmid isolation kit. However, later on i extracted the gDNA from that portion of the given organism, luckily i...

01 January 1970 9,650 4 View

Is there any online tool available which could determine the possible functional role of a microbes using 16s V3 / V4 region gene through NGS ?

I would like to determine the functional role of a non cultured or eDNA based given bacterial community. Is there any online tool available which could determine the possible functional role of a...

01 January 1970 9,821 3 View

What does 2x250 bp paired-end read means in Next Generation Sequencing on Illumina platform?

I am very naive with the Illumina sequencing and I got the sequenced raw data and report. I am quite new with the technique and terminology. Can anyone explain what it means that was sequenced...

01 January 1970 6,080 13 View

While NGS QC, Why its bad to have similar sequences in the fastq file? Wouldn't it be normal to have more than one copy of the same read?

I am new in NGS, so I have a question, why is bad to have similar sequences in the fastq file? Would not be normal to have more than one copy of the same read?

01 January 1970 9,156 2 View

Which one is a suitable tool to check the quality of NGS high throughput sequence; FastQC or MultiQC or any other tool ?

which one is a suitable tool to check the quality of NGS high throughput sequence; FastQC or MultiQC or any other tool ?

01 January 1970 3,212 9 View

How to analyze NGS 16S rRNAmetagenomic raw data?

I have Raw data sequenced on Mi-seq NGS platform, the prime objective is to analyze the diversity of the given sequences. what could be the various pipelines and methods to distinguish the...

01 January 1970 1,888 9 View

What is article processing charge and why the publication fee is charged to Author?

What is article processing charge and why the publication fee is charged to Author? is not it a burden on the authors?

01 January 1970 7,407 3 View

How to interprete the alpha diversity boxplots (Shannon, Bray-Curtis, etc.)?

I have a question regarding interpretation of alpha diversity boxplots (Shannon, Bray-Curtis, etc.). How are the whisker and box lengths determined? Does the box represent the upper and lower...

01 January 1970 8,586 3 View

What does bootstrap value denotes while constructing a photogenetic tree ?

Is bootstrap necessary for the construction of phylogenetic tree and what is the best no. of bootstrap replicates value for construction of bacterial phylogenetic tree by any method? I have seen...

01 January 1970 370 3 View

What is/are the best free database and methods for comparative metagenomic analysis (16s rRNA)?

I have to perform a comparative analysis of my metagenomic 16s rRNA data (samples) with different other regions, please suggest me different methods and database in detail .

01 January 1970 5,468 3 View

What is the total size of 18s rRNA? And what are the sequence length of each region from i.e V1, V2, V3, V4 etc?

What is the total size of 18s rRNA? And what are the sequence length of each region from i.e V1, V2, V3, V4 etc? I am working on identification of invertebrates from different environmental...

01 January 1970 2,595 1 View