Questions tagged [genetics]

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Variant vs Allele vs SNP

Coming from a CS background. Reading through the wikipedia page, these all sounds like the same thing: Variant, Allele, and SNP. Variant/Allele/SNP: Some gene locus that differs from the idea human. ...
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35 views

Research questions regarding WGS data from plant pathogens [closed]

What types of questions can be answered using whole genome sequence data?
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0answers
27 views

What is the best way to start for analysing DNA methylation TGCA datasets using R? I want to learn but I'm a novice

I am relatively new to programming and only have a basic knowledge base for R. I am keen on learning how to manipulate DNA methylation arrays for analysis related to Glioblastoma Multiforme. More ...
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1answer
55 views

Is there a Python program that is able to show convergent and divergent evolution on a phylogenetic tree?

I was wondering if there was a Python program that detects convergent and divergent evolution on a tree. I am also curious if it is just better to look at a phylogenetic tree and conclude what is ...
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0answers
37 views

How to see if a gene is the product of copy number variation?

Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals.Copy number variation is a type of ...
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1answer
57 views

How to identify unknow bacterium species from whole genome genetic sequence

I am a Biochemist that is unfamiliar with bioinformatic tools and new to academia as a whole. I am currently using ILLUMINA PE data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled ...
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37 views

Coding vs non-coding DNA length

I am trying to calculate the total exonic length (in bp) in order to see where the coding-noncoding ratio of roughly 1% to 99% comes from. We know all chromosomes total about 3 billion base pairs. So ...
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2answers
43 views

Should you filter GWAS hits with high standard error?

I'm trying to figure out if I should be filtering out GWAS hits that have high standard error and I'm not quite sure what to do. It seems like it might not matter, because the standard error is used ...
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0answers
42 views

CRISPR Screen Control - What genes do not affect phenotype when knocked out?

I have some raw read count data from a crispr screen. The library used was addgene's Mouse Improved Genome-wide Knockout CRISPR Library v2 I'm following an analysis pipeline that requires counts ...
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2answers
97 views

Detecting whether genome is genetically engineered?

Is there a methodology for detecting whether a genome has been tampered with by a biologist? For instance, say there has been an ebola outbreak such as in "The Andromeda Strain". Is there a way a ...
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2answers
55 views

Genetic Genealogy related to SNP variants and INDEL variants

Background: I am looking for some advice on the use of SNP variants versus INDEL variants for determining Genetic Genealogy, specifically for determining accurately the "START" and "END" of shared DNA ...
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1answer
67 views

Read-informed statistical phasing

I'm wondering if there are any tools out there that perform statistical phasing of genetic data (e.g. Eagle) that take read-based phasing from GATK into account. I've found this paper which sounds ...
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2answers
1k views

What is the name of this type of figure?

This figure comes from this wiki page. I googled "gene location figure" and "gene location plot", none gets similar results. I also tried search by image, none of the results is close. so, what is ...
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2answers
305 views

How to cluster the human genes by pathways/system-biology/metabolic properties?

I would like to make a chord plot from my data. I have a list of genes that according to my experiments are divided into 64 clusters of enrichment pattern. I would combine my 64 clusters with a ...
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4answers
208 views

How do you query and explore ENCODE data?

I am looking for a modular way to query data from ENCODE. For example, I would like to get CHiP-seq or similar tracks for a specific cell line. What's the proper way to do it? Finally, is there an ...
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1answer
84 views

Continuing analysis based on a log-likelihood ratio? (Comparing methylation between two PoolSeq phenotypes)

I'm trying to get some pointers on where to start on the analysis of my dataset. First, some basic info: Background: We performed Nanopore sequencing of two poolseq samples called UU and DD referring ...
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2answers
96 views

How do population genetics people define a population?

How do population genetics people define a population? Do they define it as a layman will do? say Africans, Americans, or so? Or is there a more scientific way of doing so? For example, I think ...