Questions tagged [genetics]

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Extracting base sequences from ABI/AB1 sanger sequencing chromatogram

I am trying to understand the sanger sequencing ABI/AB1 file format better, and extract base calls from given signal intensities over time. As I understand, reading in a raw AB1/ABI file into python, ...
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Could someone please help me understand the outputs for HapFlk

Could someone please explain the output file for HapFlk? My input file was a ped file which has three different populations. Two with same number of snps by imputation and third one is an outgroup ...
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How to interpret a negative beta within a binary GWAS?

I have run a GWAS on a binary trait - "Are you following a carnivore diet?" - so the cases are individuals who follow this diet, and the controls are individuals who do not follow this diet. ...
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VCF or BAM file for raw data of gene test?

My friend has a VUS (Polymicrogyria with or without VEDS) mutation that was found in her whole-exome sequencing with respect to the phenotype given that time. At present, her doctors have more ...
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1 answer
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pathogeniticy prediction tool

I have a question related to the evaluation of variant pathogenicity in the context of human genetics. There are many predictors available, however, is there a specific predictor that takes into ...
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1 answer
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Is there any genetic sequence, such that, for all the kinds of mutation, it still has a 100% probability to be passed on?

This question is more on the theoretical-encoding side. Given the known kinds of genetic mutation, transposition, deletion, and such, what can be said about genes that would be left untouched by the ...
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If I have data from a full genome sequence, how can I search for a known pathogenic variant of a known gene?

I have a CS background, but am a bioinformatics neophyte I did a full genome sequence which provided me with ~100GB of files (SNP VCF, Indel VCF, BAM, Indel TBI, SNP TBI, BAM BAI, CNV VCF, CNV TBI, CV ...
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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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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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1 answer
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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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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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1 answer
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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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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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2 answers
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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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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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2 votes
2 answers
103 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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2 answers
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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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1 answer
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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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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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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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5 votes
4 answers
239 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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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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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 ...
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