5 votes
Accepted

How can I get a list of papers where a particular mutation has been mentioned?

You could use the pubmed API to query it directly. Typically I use Biopython for my pubmed queries. There are some good examples in the cookbook and on other SO posts. This example from the ...
  • 2,576
4 votes
Accepted

How to get unique somatic mutations for each individual patients

If what you want is to split the main VCF file into 1 file per sample, you could use bcftools query and view commands. A similar question was asked on biostars, adapting Jorge Amigo's solution to ...
  • 595
4 votes

Is there a aminoacid mutation that forms similar protein?

A mutation is most often likely to be either neutral (no effect) or destabiling (protein misfolds). Changes in activity require changes at the active site or the entranceway to it —which are often ...
  • 3,854
3 votes

Why can't AlphaFold predict the consequences of point-mutations?

Other have addressed why AlphaFold2 cannot really get the necessary signal from MSA (Multiple Sequence Alignment) and memory to properly model a variant, but I thought I'd add my observations/rants. I ...
  • 3,854
3 votes
Accepted

>My counter is counting genotypic combination occurences more than once, how do I ensure it counts one combination and doesnt count it again?

Alright, so there are a number of problematic patterns in your code - as far as I understand what you are trying to do. Next time, try to post a reproducible example that people can use and more ...
3 votes

Which gene I should select from this qqplot

Given that TP53 is the most significant and is already known to have driver mutations in cancer it would seem to be the logical choice.
  • 19.3k
3 votes
Accepted

Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment

...
  • 19.3k
3 votes

Show presence of known mutation in RNA-seq data

If you only have one gene and you only need to do this once then the simplest possible workflow is to generate the aliment using STAR (optimally with the two pass method) and open the two resultant <...
  • 1,029
3 votes

Show presence of known mutation in RNA-seq data

For counting reads I use mpileup, e.g. samtools mpileup --reference hg38.fa -r Chr10:18000-45500 input.bam, which will give base-resolution coverage for a BAM file. ...
  • 12k
2 votes

Information about control data

Without control data from your subjects, I don't think there's really no way to distinguish somatic mutations from germ-line mutations. The best you can do is to screen out common variants, which are ...
  • 1,806
2 votes

State of the art mutation simulation software

Question I suspect this question is about the phylogenetics of methylation and the approach the investigator is proposing would be the last approach to use. Summary The approaches to assess the ...
  • 7,980
2 votes

Which gene I should select from this qqplot

You can't know which is the driver and which is the carrier. At most you can say that a specific gene deviate more of the expected underlying hypothesis. See also other resources online. You also ...
  • 4,622
2 votes

Error in running Mutect2

Your input file pon.vcf.gz should be a gzip file, but from your file command it looks like it is an HTML file instead. Perhaps ...
  • 2,116
2 votes
Accepted

How to calculate various properties of a protein structure per atom using PDB2PQR and Rosetta tools (or any other tools)?

Per Atom You are correct. Rosetta scorefunction does not store any per atom data. The scoring operates at the per residue level. Whereas each atom has its coordinates and properties in full atom mode, ...
  • 3,854
1 vote

Why can't AlphaFold predict the consequences of point-mutations?

As marcin points out in the comments: by "AphaFold (AF) has not been trained to predict structural consequences of point mutations" it is meant "AF is not able to tell you whether your ...
1 vote

Why can't AlphaFold predict the consequences of point-mutations?

This answer is from common knowledge rather than specific infield expertise. The question could be more expertly answered by other members. If you really want to pursue this type of calculation, it's ...
  • 7,980
1 vote

Can we do NGS library preparation using UMI with large amount of DNA input?

Whole genome sequencing uses between 50 ng and 1 μg of high-quality DNA (A260/A280: 1.7–2.0) for PCR-amplified or non-amplified libraries if your focus is precision oncology as described in the ...
1 vote

Can we do NGS library preparation using UMI with large amount of DNA input?

The question is "Do I add 20-fold more DNA than the kit states?" Its not my area - this is wet-lab - but there will be a tolerance however 20-fold is excessive (>1 log), i.e. no it ...
  • 7,980
1 vote
Accepted

Caching and parallelization

Summarising @Jesse's comment I think is the right answer, open the database outside parallelisation. What I didn't thoroughly describe (and what was essentially requested) is the architecture, the ...
  • 7,980
1 vote

Counting the co-occurrence of variants A and B in an aligned sequencing read

Related question: Access base aligned to particular reference position After an initial effort posted here, I ended up rewriting this and testing it a little, and posted the script here. It still has ...
1 vote

A unified database for CNV, SNP, Indel and MSI

To Answer my own question, one can use variation viewer to get all the information :) DisGeNet is another resource.
  • 175
1 vote

How do I create a VCF file of all known pathogenic mutations in a gene of interest?

I'm not sure how to generate the additional mutations, but I would say that HGMD is not the way to find all the pathogenic variants. I would probably filter this table by either Clinical significance ...
1 vote
Accepted

Is there a way to customize what observations are plotted in ComplexHeatmap?

What is fed into ComplexHeatmap is what it outputs! So if one of your genes has a Missense_Mutation as well as a ...
  • 3,507
1 vote

How to calculate mutation rate and mutation sites in a genome using FASTA file?

You can still align a FASTA file with a tool like bwa mem ( if they are short reads ) or minimap2 for long reads and run it through a variant caller like freebayes. Alternatively, if you have ...
1 vote
Accepted

Is there a tool for synonymous recoding of DNA sequences?

There seems to be a bioconductor package named synmut which does just that. Apparently, it can take codon usage into account when generating synonymous mutations. ...
  • 595
1 vote
Accepted

Scooping and GeneMatcher

I am having trouble finding anything that directly addresses the issue of failed collaborations leading to scooping, but here are some examples of similar behavior: it is sort of implicit in the ...
1 vote

Are there databases to annotate non-coding mutations?

VarSome allows you to annotate any variant, including non coding ones. While ACMG classification will not be available if the variant isn't in a gene's transcript (the ACMG criteria are only ...
  • 8,225
1 vote

Plot a circos plot to show the consistency between 2 samples

A circos plot is most likely not the most appropriate solution here. What I would suggest is a confusion matrix, of which you can find an example here: For every variant in your vcf you'll add a ...
1 vote

Which gene I should select from this qqplot

This looks to be a pretty good Q-Q plot. My recollection of doing Q-Q plots is that a good Q-Q requires a "more or less" linear relationship for the model to be considered okay. Again this model looks ...
  • 7,980
1 vote

how to do analysis of a table content SNP?

For working with a relatively small dataset in tabular format, I would recommend dplyr. You can read in a excel file using readxl ...
  • 1,806

Only top scored, non community-wiki answers of a minimum length are eligible