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Questions tagged [metagenomics]

Metagenomics is the study of genetic material from a mixed and often undefined community.

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How much data to expect from metabarcoding? [migrated]

I am about to conduct my first metabarcoding study. We will be using the ITS amplicon to look at fungal community composition in soil samples. I need to write a data management plan before I actually ...
Rendzina's user avatar
7 votes
4 answers
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Limitations of 16S rRNA sequencing

Looking at the microbiome analysis literature there seems to have been a shift away from 16S rRNA sequencing analysis toward shotgun sequencing of the whole genome. While the motivation given is ...
gcorso's user avatar
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2 answers
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Can the metatranscriptomics replace the approach of functional metatranscriptomics/functional metagenomics?

While metatranscriptomics reveals information about the expression of genes and their functions too, Functional metatranscriptomics (https://www.nature.com/articles/ismej201167) allows the ...
Noor Elhouda's user avatar
2 votes
1 answer
158 views

DNA extraction kit for microbial mats, rocks, and soil in a remote area

I am hoping to perform a metagenomics study of samples from a lava tube. It will be in a remote area (with no large scientific equipment) and I would need to bring all scientific equipment myself. For ...
thatbat's user avatar
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1 answer
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16S sequencing: pooled or individual samples?

I am planning to run 16S sequencing on a set of individuals to explore microbial diversity. The question I am facing is: should I sequence them individually or I pool them (for example 5 individuals = ...
RP95's user avatar
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-1 votes
1 answer
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How to download omic data from ncbi? (SRA data or any suggestion?)

I proposed myself to replicate the results in this paper with an accession number PRJNA325650. So, I'm trying to download the data. Which will be the best way to do this?. I tried with the sratoolkit, ...
Adonis Cedeño's user avatar
0 votes
1 answer
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identifying OTU interactions / hubs

I would like to know how can i run a network analysis for identifying major OTUs hubs. I wish to build a network of co-occurring OTUs found in different soils samples. I've started going through the ...
Ziv Attia's user avatar
-1 votes
1 answer
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How do different genes on human genome express themselves?

It is said that human genome contains over twenty five thousand genes, How many of these (can) express themselves as an external or internal trait in human beings (for e.g. like eye-colors, hair ...
Aryan Gupta's user avatar
3 votes
2 answers
148 views

Could bacteria and phages be found in tissues?

in the literature, there are several studies of the gut virome and microbiome, for instance Reyes et al. on Nature (https://www.nature.com/articles/nature09199?error=cookies_not_supported&code=...
Gigiux's user avatar
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2 votes
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Methods for microbial identification in soil

I'm trying to perform a survey of the life in a soil sample. I want to know what species of bacteria, fungi, and other organisms are in it. I've heard that ITS sequencing and 16S rRNA sequencing are ...
blueintegral's user avatar