7 votes

How do you query and explore ENCODE data?

I don't know whether there is an API, but ENCODE's website does provide an interactive data matrix where you can filter data based on assay and sample type, place data sets in a "shopping cart", and ...
6 votes
Accepted

What is the name of this type of figure?

This kind of visualization showing the banding patterns of chromosomes are called "chromosome ideograms". You can use for example IdeoViz in R to generate them.
  • 828
5 votes

How do you query and explore ENCODE data?

You can just add /?format=json to any page to get the JSON output. ENCODE REST API documentation: https://www.encodeproject.org/help/rest-api/ Example scripts: ...
  • 2,109
3 votes

pathogeniticy prediction tool

Venus I am the developer of venus.cmd.ox.ac.uk, which is a site that given a mutation makes the variant (and gives the ∆∆G) and shows what residues are nearby and whether these appear in clinVar or ...
  • 3,874
3 votes

Variant vs Allele vs SNP

Variant = a locus in the genome where there are differences between individuals Allele = one of the possible bases/sequences that can occur at the variant SNP = single nucleotide polymorphism, a type ...
3 votes

If I have data from a full genome sequence, how can I search for a known pathogenic variant of a known gene?

I'm going to try and keep this answer from going overboard while still helping you find your feet. The good news is that it sounds like you have started off with some of this work already done for you,...
3 votes

What is the name of this type of figure?

Such a figure is called ideogram, or chromosome ideogram.
  • 3,551
3 votes

How do population genetics people define a population?

A population is defined as a group of people (or organisms of the same species) living together in a geographical region. However, for human genetic studies, it is wise to use ethnicity as well (so ...
  • 3,551
2 votes

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

I assume you don't want to spend 1-2 years developing your own method based on nanopore data, so the path forward is to convert the output into a format used by standard DMR calling programs. There's ...
  • 19.3k
2 votes
Accepted

How do population genetics people define a population?

It really depends on the study and the ethnicity. Mostly they use self-defined ethnicity and often they will require that three or four grandparents are of that ethnicity. Here's some detailed info on ...
2 votes

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

To measure if two genes are functional similar I developed the BioCor package. It calculates a similarity score between genes by the measuring the amount of pathways shared. However, it doesn't take ...
  • 4,622
2 votes

Detecting whether genome is genetically engineered?

The definition of a GMO for example UK GMO regulatory bodies (HSE) is strictly the artificial introduction of foreign genetic material using targeted genetic engineering, such as splicing, genome ...
  • 8,320
2 votes

Is there any book or reference that explains evolutionary dynamics and fixation probability?

I'm fond of Joe Felsenstein's book on evolutionary genetics as a relatively recent source that presents a lot of these problems at a very simple level for the newer student, and then adds complexity ...
2 votes

Is there any book or reference that explains evolutionary dynamics and fixation probability?

Maynard Smith, J. (1989) Evolutionary Genetics. Oxford: Oxford University Press. ISBN 0-19-850231-1 Maynard Smith, J. and Harper, D. (2003) Animal Signals. Oxford University Press. ISBN 0-19-852685-7[...
  • 8,320
2 votes

From RNA-seq raw counts to normalized data

However, because I know the steps of TPM normalization in theory, one should firstly normalize to gene length, and then to gene depth. No, you should normalize to transcript length. Which requires ...
  • 1,772
2 votes

How do you query and explore ENCODE data?

So let's say I want to get the bed file of this experiment using curl encodeproject.org/experiments/ENCSR000CKC You can also search for files that belong to a ...
1 vote

Is there any genetic sequence, such that, for all the kinds of mutation, it still has a 100% probability to be passed on?

Not in the way you suggest: a sequence of letters with the property of being immutable by any type of permutation on its constituent bases. I would be interested if anything of the likes exists in ...
  • 527
1 vote

Why are genetic algorithm chromosomes represented using 8 bit binary?

Not always. The representation of chromosomes in genetic algorithms is often dependent on the specific problem to be solved and number of variables to be found through the optimization process. Not ...
  • 527
1 vote
Accepted

How to interpret a negative beta within a binary GWAS?

Negative beta means that the trait under test is negatively correlated with the allele. What this actually means in relation to your specific question will depend on how the trait is coded and how the ...
  • 12.3k
1 vote

VCF or BAM file for raw data of gene test?

First of all - I would advise you against concluding anything out of your own analysis of the data, you need to consult someone with appropriate training! Can you get both? The ...
1 vote

Variant vs Allele vs SNP

First some basic biology, taking human as an example. Humans have 22 chromosomes (image source): As you can see (if you squint) in the image, we have two copies of each of the 22. With the exception ...
  • 8,525
1 vote

Variant vs Allele vs SNP

Just to add on to previous answers, it is important that allele is one of the possible versions or sequences that can happen at a given position. Take SNP. Most SNPs have two alleles, meaning that in ...
1 vote
Accepted

Genetic Genealogy related to SNP variants and INDEL variants

InDels are just as informative, but are less reliable to call. Errors should be averaged out in this kind of analysis though (so long as they don't predominate). Both SNPs and InDels are valid data ...
1 vote

Read-informed statistical phasing

shapeit4 is currently (probably) the most accurate and quickest phasing algorithm which can account for sequencing reads in the model. They suggest you extract the phase information from the reads ...
  • 1,288
1 vote

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

Well in the absence of a definition of 'divergent evolution' I would simply use a definition of allopatry. If the divergence is congruent with geographic distance or geographic foci this provides some ...
  • 8,320
1 vote
Accepted

How to identify unknow bacterium species from whole genome genetic sequence

You can use KmerFinder and Kraken2 for taxonomy assignment
  • 759
1 vote

Should you filter GWAS hits with high standard error?

I am curious about the relationship between your p-value (or effect sizes) and standard error. I would expect the significant signals to have smaller stand error compared to the non-significant, ...
1 vote

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

Production of a chord diagram is described in detail here. You use the R package with either, library(chorddiag) library (circulize) The first level clusters ...
  • 8,320

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