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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Barrett's esophagus databases and web tools
I would like to ask if anybody knows public domain databases and web tools to analyse different stages of Barrett's esophagus. The most that I can find are esophageal cancer databases with patient's ...
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1answer
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How do you find differences when your metagenome sample size is small?
I received a matrix of genomics features (KEGG annotated metagenomes) abundance from 6 samples belonging to 2 groups. My collaborator is interested in finding differences between the two groups.
The ...
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1answer
38 views
Converting FASTA Sequences to SNP FASTA Format
I have two FASTA sequences. Each is from a different species' mitochondrial genome. The sequences are pasted below.
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1answer
23 views
how to get access to genotypes and phenotypes used for a GWAS
I'm a master's student working on genomic prediction of complex traits using deep learning.
i'm looking for a dataset of human genotypes and phenotypes that has been used for a GWAS.
The only thing i ...
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2answers
47 views
Finding SNP/Indel Markers of Interspecific Variation
This is a revised version of my original question, edited to include the portions already answered by @Maximilian Press.
Goal:
Find SNP and indel alleles which are fixed between but lack polymorphism ...
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1answer
40 views
How do I create a VCF file of all known pathogenic mutations in a gene of interest?
I would like to create a list (probably .vcf format would be good) of all known pathogenic missense mutations in a human gene of interest and then add other variants that could lead to the same ...
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40 views
Nvidia Parabrick fq2bam pipeline error - No such file or directory
I am trying to implement Nvidia-parabrick fq2bam pipeline to process my WES dataset. The reason for opting this pipeline is the huge number of samples (1004) which take many months to process for ...
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1answer
40 views
How to count RNA sequencereads using custom made python scripts?
I am trying to do RNA seq analysis and my goal is to filter gene counts less than 5 using custom made python scripts. The code chunk goes as follows
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25 views
Genomic relationship matrix explanation
I am seeking the definition of the genetic distance matrices used in genomic prediction.
What is the difference between a Rodger distance and kinship matrix?
what people mean when they talk about ...
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24 views
make recombination genetic map
Given a Plink genetic map with 4 columns: Chromosome, rs-snp, Map(cM), Position(bp) and approximately 8,000 lines find the recombination rate [Rate(cM/Mb)] from a HapMapII genetic map of 4 columns: ...
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40 views
How to extract certain genes including non-coding regions?
I would like to look at the non-coding regions of some genes. I have around 1000 full genome assemblies and I was able to extract the nucleotide sequences for certain proteins with ...
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When to use Ariba vs Roary or other genomics tools to call drug-resistance variants?
I have a large dataset of assemblies of bacterial S. aureus genomes (~1000, same species). I am looking at different tools to estimate the presence of drug-resistance factors such as blaZ or ampC. ...
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1answer
85 views
What are the coordinates of the extended major histocompatibility complex (xMHC) in GRCh38?
Is there an accepted boundary of the extended major histocompatibility complex (xMHC) in human? Specifically, I am interested in the boundary coordinates for Genome Reference Consortium Human Build 38 ...
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1answer
36 views
How to find Genotype, from list of mutations:lineage list?
I'm very new to python and I'm getting along nicely (I'd like to believe); however, I must be missing something here. I'm looking to read each and every file and compare each line against one another.
...
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1answer
63 views
How to get % similarity between strains and mutation files
I’m very new to python, and having some difficulty getting hang of some more complicated things
I have multiple files which look like so:
hCoV-19/Singapore/4/2020|EPI_ISL_410535|2020-02-03
hCoV-19/...
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1answer
42 views
How to identify unknow bacterium species from whole genome genetic sequence
I am a Biochemist that is unfamiliar with bioinformatic tools and new to academia as a whole.
I am currently using ILLUMINA PE data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled ...
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1answer
45 views
Pointing Cromwell to local EBS mounted storage on AWS Batch
I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend.
I store the STAR alignment index on an Elastic Block Store since my Cromwell server instance ...
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1answer
65 views
COVID-19 GWAS: what is a cross-replicating association?
In a genomic study of patients infected with SARS-CoV-2, the authors detected cross-replicating associations with rs11385942 at locus 3p21.31 , the association signal spanned the genes SLC6A20, ...
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Filtering out nonarthropod sequences using Blobtools2
I am using Blobtools2 and am working my way through the sample dataset that they provide before using my own. The filtering tutorial I am following is --> https://blobtoolkit.genomehubs.org/...
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1answer
36 views
How to annotate gene length to a list of gene symbols using UCSC data?
I have a list of HGNC gene symbols, I am looking to get the gene length of each gene. Although I also describe these genes with lots of UCSC datasets as features, so I am wondering if there is a ...
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14 views
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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34 views
“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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1answer
63 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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2answers
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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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29 views
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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46 views
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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1answer
19 views
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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2answers
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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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1answer
80 views
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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1answer
40 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 indexing which is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All ...
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1answer
36 views
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
37 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
78 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
60 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
143 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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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
65 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
613 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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1answer
164 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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1answer
100 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
87 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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2answers
105 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
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?
