Questions tagged [genomics]
Genomics is an interdisciplinary field of science focusing on the structure, function, evolution, mapping, and editing of genomes.
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How to decide the parameters and parameter values when running ChIP-seq Peak Calling for H3K27ac data in MACS?
I have alignment data in SAM files from ChIP-seq analysis for H3K27ac mark. I need to call peaks using MACS2. But I'm having issues with selecting parameters and values of the parameters. I will be ...
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What are the largest fully publicly available molecular QTL datasets?
I'm familiar with the sQTL and eQTL GTEx data that can be downloaded from the
GTEx Portal, but I'm interested in gathering at least two other types of molecular QTL datasets:
Larger eQTL and/or sQTL ...
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1answer
34 views
What does these terms mean?
I am working on cancer genomics failed to follow some terms even by googling
What is the difference of focal genome amplifications versus convergent amplification of given region of genome for ...
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2answers
71 views
CRISPR screening and systems biology
I am not sure how to tackle this one, so I’ll explain the general idea I have in mind.
Given results of a CRISPR knockout screening experiment (like in this paper) with two types of assays: control ...
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1answer
27 views
How to extract hypervariable region of mitochondrial dna from its fasta file?
Recently I've done some analysis on Human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed ...
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1answer
50 views
Are there genomics databases for neurological and psychiatric disorders?
Are there databases that relate genetic disorders with neurological disorders?
I am thinking of something like COSMICS for cancer? AFAIK cancer usually develops due to a combination of 5-10 ...
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2answers
56 views
Python module for fetching NCBI id for a list of species
I have a list of scientific names of species. Is there a python module that can fetch NCBI taxonomy IDs?
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31 views
How to apply RDP, Greengenes and other special taxonomies in Krona?
I used Kraken 2 to classify my 16S metagenomic data using both RDP and Greengenes database. As these are special databases the taxonomic ids assigned do not match with the NCBI taxonomic ids. I found ...
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2answers
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 ...
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1answer
28 views
Error Viewing file on HiGlass
I am implementing hi-glass python on Jupyter, and upon running the test data code
...
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2answers
220 views
What do the FASTQ file names mean here?
I would like to run an analysis on Nanopore data. I'm trying to download sample data from https://github.com/nanopore-wgs-consortium/chm13. I would like to run minimap on the FASTQ files, resuling in ...
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56 views
creating population AF from set of individuals in 1000 genomes population?
What's the recommended way to create population-level Allele Frequency variant entries from a set of individuals (vcfs?) in the 1000 genomes (or similar) project?
For example, given the IBS ...
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57 views
what is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets?
What is the most complete vcf file of population allele frequencies that can be built/downloaded from public datasets nowadays?
About 5 years or so ago, it used to be the latest release of the CSHL ...
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1answer
81 views
Generating DNA sequences with constraints
I would like some advice on potential strategies to address the following problem.
I want to write a program that will generate DNA sequences that are optimized on two constraints based on an input ...
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1answer
72 views
Transcription factor targets for Human and Mouse genes
I want to get transcription factor targets for my list of genes (For Human and Mouse)
I have found ENCODE Transcription Factor Targets database (The link is given below). But I am looking for some ...
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1answer
50 views
Highly variable elements?
Which type of genomic elements in the UCSC browser can be used as an example of the highly labile = highly variable = low conservation regions?
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1answer
56 views
Does UCSC definition for telomere making sense?
UCSC provides a database of telomere regions for each chromosome:
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz
It reported the telomere section in chr21 as:
...
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1answer
52 views
Repetition-free Longest Common Subsequence as similarity measure
I'm starting a thesis in Computer Science with topic the RFLCS (Repetition-free Longest Common Subsequence). I know very little about Bioinformatics problems and Genomics. I would like to understand ...
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1answer
61 views
Are there any Genome in a Bottle-like resources for non-humans (especially for invertebrates)?
Genome in a Bottle is an excellent resource that provides many types of DNA and RNA sequencing reads for a single individual/cell line to test genome assembly and analysis tools. For example there are ...
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2answers
222 views
Selecting 65000 SNPs where AF is close to 0.5 in all or most populations
I am evaluating the tool somalier (https://github.com/brentp/somalier) and I need to create a list of about 65,000 SNPs where the allele frequency (AF) is as close to 0.5 as possible across the most ...
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2answers
114 views
Genomics Statistics Problem
I have used a python script to identify target sequences in a DNA sequence file. There are two classes of sequence: coding and non-coding.
I have identified 728 sequences of interest. 597 of these ...
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1answer
180 views
Proof of Breakpoint Reversal Sorting Approximation Algorithm
I'm kind of new to bioinformatics and trying to self-study. I'm reading a bioinformatics book: An Introduction to Bioinformatics Algorithms and ran into some problems about understanding the proof of ...
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1answer
76 views
Are there free cloud computing platforms for biology projects? [duplicate]
I want to implement the analysis found in the paper RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics The project id is 281708. ...
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1answer
123 views
How to find all variable-length seqs with an exact 5' and 3' match in a FASTA file
Context
I am interested in finding all of the promotors specific to a particular sigma factor. I have identified the -35 and -10 sites from the literature, bold denotes -10, -35, binding sites:
<...
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1answer
156 views
ANY (technical) reason behind submitting sequences to GenBank versus ENA Sequence
The DNA sequence sections of the three INSDC databases (i.e., DDBJ, ENA Sequence and GenBank) are synchronized periodically and strive to keep their stored data as ubiquitously accessible as possible. ...
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1answer
35 views
Genomics: Downloading genomic data from the NCBI Genbank database
I'm taking a genomics course at school, and we have a final project due in a few weeks.
Now, I can write bash scripts to sort and analyze the data, etc. However, I'm not quite sure how to actually ...
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57 views
Colinearity analysis with respect to gene orientation
I was reading the manual of MCScanX and found that besides a all-vs-all protein blast file the tool takes a gtf file with four columns only: scaffold name, protein name, from, to.
As the tool is not ...
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29 views
Python module bamtags
Does anyone know this python module, bamtags? I'm using a pipeline (Dovetail Genomics, HiRise) that imports it, but it seems it doesn't exist.
It's impossible to install it and there is no ...
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0answers
624 views
Searching for start and stop codons for protein sequencing of contigs
I need to convert contigs into their respective protein sequences given a reference genome (i.e. I need to take a substring, whose position is already known on the string, and I need to locate the ...
3
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1answer
59 views
How to query the Human Microbiome Project (HMP) to find all subjects with both 16s and WGS workups?
I am looking for a query to run on the HMP database that will return all subjects who have had BOTH 16s and whole genomes sequence (WGS) workups. I am currently using this query...
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2answers
55 views
Genomic coordinates of predicted binding pocket
I would like to know the genomic coordinates of a proteins ligand-binding pocket. For example, on this PDB page you can see that there is xray crystallography data for how CYP2C9 interacts with two ...
3
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1answer
149 views
Path to career in bioinformatics?
I've been completing various courses on bioinformatics through edX and Coursera, and I've made a strong footing in the material.
I'm not sure what to pursue next in bioinformatics that would bring ...
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Meaning of category in MutSigCV
I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is category. According to MutSigCV, every mutation can be divided into the following ...
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1answer
133 views
Meaning of the FORMAT fields of the VCF file coming from GIAB project
After reading the GIAB paper in https://www.biorxiv.org/content/early/2018/05/25/281006 and its Figure 1, I am still having trouble understanding the data inside the GIAB VCF file for HG001 (...
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1answer
164 views
How to download SNP data from specific regions, population and positions?
I am totally new in Bioinformatics and I would like to apply my knowledge in feature selection on the tag SNP problems.
To do that, I've read a lot of papers and books in order to understand the main ...
3
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1answer
77 views
Difference between copy number neutral reads and active reads
In this paper, the authors talk about copy number neutral reads (as reads that equally represent parental chromosomes) and active reads (as reads from only one parent chromosome):
We reasoned that ...
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59 views
“Cleaning up” a gene heatmap in R
I'm using the ComplexHeatMap function from Bioconductor to display a heatmap showing the presence/absence of hundreds of loci of interest, but I need to clean it up ...
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48 views
Complete Genomics Junction file for SV Detection
At present, I have vcf file for each patient generated from tumor data. I am using virtual normal correction method for somatic mutation detection because I don't have normal data. For SNP or small ...
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1answer
223 views
How can I improve ESS values for ucldMean in beast?
Using starBeast I ran a 50 locus tree, with 34 individuals, using evolutionary models indicated by AICc in jModel test. I ran this tree with a MCMC chain length of 500 million, storing every 10,000 ...
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1answer
157 views
Is it possible to use SNP heterozygosity as a proxy for Indel heterozygosity?
I have estimated genome-wide heterozygosity levels using maximum likelihood and classical substitution model implemented in package atlas. These estimates are way more robust than classical SNP ...
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1answer
212 views
Command not found error on HISAT2
I have been attempting to map reads to a reference genome using HISAT2 using the Pertea, et al 2016 Nature Protocols paper. I am able to successfully generate an index (using the hisat2-build command),...
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125 views
How can I calculate and compare intra-cluster correlation for each GO term and pathway?
How can I calculate and compare intra-cluster correlation for each GO term and pathway?
I want for all the genes, which belong to the same GO-term, calculate a similarity score. Each GO term can be ...
3
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1answer
54 views
predict the foldability of single-stranded DNA molecules
I have a list of regions of the human genome and I want to predict if single-stranded molecules in a buffer would tend to fold and create pin structures by sequence self-complementarity. What's the ...
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1answer
352 views
ethnicity check either from bam or vcf files
What tool could I use to check the ethnicity of a human bam or vcf file? I would like to use the results as a QC check to know whether a given sample or set of samples match the ethnicity information ...
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2answers
3k views
What are the differences between GWAS and QTL mapping? [closed]
What are the differences between the two methods?
What advantages does one have over the other, and what are their limitations relative to one another?
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1answer
134 views
What does “motif 2 bp or longer” mean?
I'm reading a preprint on a new somatic variant discovery tool, and the first sentence of the Discussion section has me confused.
Across the four datasets analyzed in this study, we discovered that ...
5
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3answers
820 views
Somatic tumor only variant calling?
I'm evaluating possibilites for somatic tumor variant calling without paired-normal samples. I'm aware of the consequences without a normal sample.
All the popular variant calling tools such as ...
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1answer
76 views
Installing Sibelia for Ragout on Mac OSX
I am trying to use Ragout: https://github.com/fenderglass/Ragout
to fill the gaps in my de novo genome assembly. You can access the article freely here: https://www.ncbi.nlm.nih.gov/pubmed/24931998
...
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1answer
353 views
Using BLAT command line tool to blat split sequences
I have the nucleotide sequence:
AATTGAGGCACATTTTTTTTTAGACAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGTGTGATCATAGCTCACTGCAGCCTCGACCTCCTGGGCTCAACAAAGCACACAGTGGGCGGATCCCCACCAG
When I blat this on UCSC Genome ...
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3answers
240 views
How to adapt the fgseaL function to perform rapidGSEA computation of gene ranks across 9 different phenotype labels?
I wish to adapt the r language function fgseaL, https://github.com/ctlab/fgsea , to perform rapidGSEA, https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1244-x , computation of ...
