Ishtiaque Ahammad

10 Questions 17 Answers 0 Followers

Questions related from Ishtiaque Ahammad

Can the amplicon size be shorter than the sequencing read length in 16s rRNA sequencing?

I have found a dataset where the 16rRNA amplicon size is 292 bp while the sequencing reads are 300 bp. Is it possible or is it a mistake by the people who uploaded the data in NCBI?

26 May 2022 6,288 3 View

Can you a suggest a good tool for visualizing a de novo assembly of a large mammalian genome?

I have used QUAST for visualizing prokaryotic genome assemblies and they worked fine. But for some reason, it is not working for a large eukaryotic mammalian genome assembly. Is there any...

22 April 2022 2,079 2 View

Can you a good tool for calculating N50 statistic of a large mammalian genome?

Suppose you do de novo assembly of a mammalian genome. How do you calculate the N50 value? I have tried quast but its fails probably because of the huge size of the genome.

22 April 2022 5,084 5 View

How do I get alpha diversity and beta diversity from shotgun metagenomic data?

Please suggest a tool that can provide alpha diversity and beta diversity of microbes from shotgun metagenomic data either from raw sequences or assembled contigs.

25 January 2022 7,781 2 View

How can I prepare a bilayer with a receptor-ligand complex in CHARMM-GUI for doing simulation in GROMACS?

I have successfully made a bilayer with just a receptor for simulation in GROMACS and it works. However, when I try to make a bilayer with receptor-ligand complex in CHARMM-GUI, it fails. How can...

17 August 2021 4,052 0 View

Which tools can I use to check the quality of metagenomically assembled genomes? And how do I refine and validate them?

After metagenomically assembling bins, how do I check their quality? is there any tool to improve their quality? Are there any tool to validate the genomes?

13 July 2021 8,493 4 View

How do you find out which species' genomes metagenomically assembled "bins" correspond to?

I have assembled "bins" from metagenomic samples. But is there any tool that can tell me which species do these bins/putative genomes belong to?

13 July 2021 3,514 8 View

Which one is a good binning tool for constructing metagenomically-assembled genomes?

Also if you could give a pipeline for constructing metagenomically-assembled genomes from shotgun sequencing data, that would be great. Thanks in advance.

09 July 2021 235 4 View

How to solve the GROMACS error "One or more water molecules can not be settled" during energy minimization?

During the energy minimization of a protein before Molecular Dynamic Simulation in GROMACS software, I am getting this error: "One or more water molecules can not be settled in GROMACS". Just...

18 May 2021 4,483 10 View

Molecular Dynamic Simulation error in GROMACS version 2020.1 (PME rank 2 are more than 2/3 times the cut-off). Is there any solution to this?

I'm running a protein-ligand Molecular Dynamic Simulation but getting the following error after hitting mdrun. Can anyone offer a solution to this? Thanks in advance. Fatal error: 66 particles...

04 February 2021 1,525 4 View