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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Swapping to effect increasing allele in case/control studies

I want to find the effect-increasing allele for a given set of SNPs. For quantitive traits, I understand the effect sign is changed when the A1 and A2 are swapped. How does this work for odds ratios? ...
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“How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?”

I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I ...
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41 views

How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features from UCSC genome browser (e.g. number of CpG ...
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How identifiable are human omics data and how to mitigate their identifying features?

Say a database were to store human omics datasets. The human subjects are known and the sample size is rather small in size initially (n=500). The database contains genomics, transcriptomics, ...
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Kraken2 > OTU format > Phyloseq

A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION. I would like to use this data in phyloseq, however, I ...
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What is the origin of the 'source Gene ID' references given in the 'gene_presence_absence.csv' output of Roary?

I am learning to use Roary for preparing a pan genome for some lactobacillus strains. In the 'gene_presence_absence.csv' output of Roary (which i view in excel), a 'source Gene ID' is given for each ...
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How do I delete ligands from a list of 50,000

I need to delete ligands from a list of over 50,000 ligands in a .sdf file format. Is there any easy and quick way of deleting the ligands from the list. Thank you, Dr. Hussain.
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How to aggregate multiple MAF files together?

I have cancer genomic data (tumor/normal whole exome sequencing) from 50 patients that received the same type of treatment, half of whom responded. These come in the form of 50 .maf files, along with ...
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Is the number of contigs and scaffolds an artifact of genome assembly and rather arbitrary, or is it canonical for each species?

E.g. bowhead whale genome has X contigs and Y scaffolds, but couldn't these easily be different numbers?
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How to combine two Genome-wide Association Study (GWAS)? [closed]

I did a GWAS analysis in the past for antibiotic resistance of E. Coli and the results were interesting (matching the literature). I did a new GWAS analysis for some new samples, but the results are ...
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Problem with classification model of genomic data: every machine learing model predicts wrongly almost always the same subset of dataset

First of all, I'd like to apologize for any spelling or grammar mistakes. I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
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Phasing partially phased genomic data

I am trying to create an integrated callset with coding regions from phased exomes and noncoding regions from a genotyping array. I would like to merge the data together in the correct phase. Since ...
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Coding object structure properties into a sequence

Hopefully, I found the right place to ask. Please, note that I'm not a specialist in the current field. Is there an algorithm to code information about object structural properties into a sequence (...
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35 views

How to compute Shanon entropy

I want to analyze some viral sequences. I want to use shanon entropy as a measure to analyze the sequences. However I do not understand the concept of shannon entropy. Would anyone explain please how ...
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What Cellbase resources are 0-indexed, and which are 1-indexed?

The UCSC Genome Browser Team is clear about that the genome browser GUI is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All UCSC tables are 0-...
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Mapping a disease integrome on the whole genome

I'm currently studying a disease which has complex traits (non mendelian disease). Very few data are available on humans. But data collected from cell/animal models have been used to identify human ...
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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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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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76 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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49 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
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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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3answers
105 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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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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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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Error Viewing file on HiGlass

I am implementing hi-glass python on Jupyter, and upon running the test data code ...
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353 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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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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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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84 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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80 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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51 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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66 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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53 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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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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236 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
118 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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268 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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78 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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133 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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182 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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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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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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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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786 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 ...
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1answer
60 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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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 ...
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1answer
153 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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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 (...