Questions tagged [genetics]
The genetics tag has no usage guidance.
32
questions
2
votes
0
answers
11
views
Calculation of Site Frequency Spectrum (SFS) using STR data
Hi everyone I had a question on if it is possible to calculate (Site Frequency Spectrum)SFS using STR data. Please mention if you know any programm that can be used for that!
I have tried Arlequin but ...
- 21
0
votes
0
answers
22
views
Filter VCF file for most differentiated SNPs (Fst) in VCFTools
I have a filtered VCF file that I want to subset for the 500 most differentiated SNPs based on estimated Fst values (calculated in vcftools). I am not completely sure how to approach this. I have ...
- 21
1
vote
0
answers
34
views
DATES: sh: 1: dates_jackknife: not found
I've been trying to run DATES, a software that estimates admixture time, on my Linux Mint machine but I keep running into problems. This is the code to run the program:
...
- 11
1
vote
1
answer
39
views
How can I use sequences with different lengths in arlequin?
I have mtDNA sequences of the cox1 gene from various populations of one species. I want to perform an AMOVA allele frequency analysis via Arlequin. This allele frequency package however requires my ...
- 127
1
vote
2
answers
32
views
Is there any book or reference that explains evolutionary dynamics and fixation probability?
I am a master's student in computational and mathematical biology, with a bachelor's degree in pure mathematics.
I am really struggling with my computational biology course, we are supposed to study ...
1
vote
1
answer
243
views
From RNA-seq raw counts to normalized data
I have several RNA-seq datasets. Some of them provide RNA-seq raw counts, some provide FPKM, RPKM and some have transcripts per million (TPM) data. Non of them provide fastq files, all data is ...
- 111
0
votes
1
answer
75
views
Why are genetic algorithm chromosomes represented using 8 bit binary?
I am learning about genetic algorithms.
Why chromosomes are represented using 8 bit binary.
This arose when I apply crossover techniques to the bits.
Please help me to find the answer.Thanks in ...
- 1
2
votes
1
answer
82
views
Find SNPs in yeast genomes
I'm a new Bioinformatic scientist working for a yeast genetics company.
Objective To create a database of yeast genomes from NCBI and identify SNP variants.
In my pipeline
FastQC,
Trimmomatic,
BWA
...
- 494
1
vote
0
answers
18
views
Which components must be included in the HDR plasmid?
I am trying to design a plasmid for our knock in experiment and wanted to clarify some technical issues.
I wanted to know exactly which components must be included in the plasmid.
I know that I have ...
1
vote
1
answer
308
views
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, ...
- 11
0
votes
0
answers
24
views
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 ...
- 1
1
vote
1
answer
162
views
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. ...
- 155
1
vote
1
answer
172
views
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 ...
3
votes
1
answer
53
views
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 ...
- 31
0
votes
1
answer
56
views
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 ...
0
votes
1
answer
157
views
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 ...
- 101
4
votes
3
answers
4k
views
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.
...
1
vote
0
answers
29
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 ...
1
vote
1
answer
148
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 ...
- 11
1
vote
0
answers
44
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 ...
- 137
1
vote
1
answer
135
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 ...
- 113
0
votes
0
answers
44
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 ...
- 1
0
votes
2
answers
83
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 ...
- 841
1
vote
0
answers
46
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 ...
- 219
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 ...
- 159
1
vote
2
answers
78
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 ...
1
vote
1
answer
68
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 ...
- 841
1
vote
2
answers
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 ...
- 123
0
votes
2
answers
459
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 ...
- 1,417
5
votes
4
answers
263
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 ...
- 1,417
1
vote
1
answer
125
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 ...
- 11
5
votes
2
answers
128
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 ...
- 511