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 ...
- 5,110
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.
- 886
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: ...
- 2,209
4
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 ...
- 1,779
4
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,...
4
votes
Accepted
Find SNPs in yeast genomes
for illumina reads (only)
prerequisite: download n prepare
the fna n gff file of yeast reference
mapping_in_02.directory
1st step is mapping the downloaded reads to the reference genome:
build ...
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 ...
- 4,274
3
votes
What is the name of this type of figure?
Such a figure is called ideogram, or chromosome ideogram.
- 3,601
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 ...
- 3,601
3
votes
DNA sequences of random base pairs
You seem to have learned that what genomics terms mean by "low complexity" seems to be quite different from what you mean- it is in fact specifically not random.
There are of course many ...
- 4,252
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 ...
- 19.8k
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 ...
- 1,779
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 ...
- 4,721
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 ...
M__♦
- 13k
2
votes
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 ...
- 10.6k
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 ...
- 4,252
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[...
M__♦
- 13k
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 ...
- 2,061
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 ...
- 21
2
votes
Accepted
tensorQTL interaction issue
Writing a solution for anyone interested. The issue stems from a dosage error, some variant contains only heterozygous individuals and no homozygous ones needed for QTL calculation.
I used plink2 to ...
- 51
2
votes
How do I compare multiple cancer datasets to find the common and unique genes and difference in gene expression among them?
A few points:
Firstly, VScode isn't comparable to R. The former is a text editor with a lot of available third-party plugins. The latter is a programming language for statistical analysis. For all ...
- 214
1
vote
DATES: sh: 1: dates_jackknife: not found
I suspect the path should not be 'ubuntu/home/Desktop/DATES/bin'. It should be /home/username/DATES/bin, where username would be your ubuntu ID/name
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 ...
- 857
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 ...
- 857
1
vote
Extracting base sequences from ABI/AB1 sanger sequencing chromatogram
You can access the peak positions of Sanger Sequencing chromatograms from ["PLOC1"].
The position values in ...
- 111
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 ...
- 15.1k
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 ...
- 5,652
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 ...
- 887
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 ...
- 188
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 ...
- 1,789
Only top scored, non community-wiki answers of a minimum length are eligible