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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General Question: Statistical Alternatives to Oncoprint
I am a computational genomics student who has recently joined a research lab as an RA. We often work with oncoprints (comuts/heatmaps), and we visualize molecular signatures by reorganizing the comut. ...
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Parallelizing microRNA targets
I am trying to look for miRNA targets using a file called Conservedfamily.txt from the Zebrafish target scan fish website. I have written a python program to ...
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How to download data from SRA in Linux systems via the command line?
My workflow for downloading data from SRA has been the following:
Access SRA Run Selector.
Enter the accession number for the project of interest.
Download "Accession List" for the "...
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How to modify dot plot in MUMmer 3 for bacteria comparative genomics?
I was trying to make a dotplot to visualize genome-genome sequence alignment by using the MUMmer 3 software (it is typically used to compare whole genome sequences of bacteria). I runned the same ...
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Conversion of SAM to BAM files
I am very new to micro RNA analysis. I have been using H. sapiens, GRCh38 + major index as given in the Bowtie Website to align with my trimmed FASTQ file .
The command I am using to make very ...
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using Bowtie to map miRNA-seq data to rfam and also reference genome
I am using Bowtie to remove non-coding RNAs (tRNA, snRNA, rRNA) by rfam and also maping our microRNA-seq data with mirbase using following code:
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RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation
I have some transcriptomic (Whole) sequencing data that I should analyse. I would like to do raw data alignment to a reference genome taking into account the multi mapped reads and uniquely mapped ...
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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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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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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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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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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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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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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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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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Parsing PLINK recombination genetic map
I have 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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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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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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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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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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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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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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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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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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"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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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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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 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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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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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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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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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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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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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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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 minimap2 on the FASTQ files, resulting ...
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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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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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