Tag: snp

Genetic diversity of loquat (Eriobotrya japonica) revealed using RAD-Seq SNP markers & More Science News

Our research analyzed the genetic diversity of 95 cultivars and strains of loquat collected from everywhere in the world. On the premise of the evaluation of the inhabitants construction of 19 Chinese loquat cultivars and strains by RAD-Seq, Hubei Province in China has been recommended as the middle of origin…

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Postdoctoral Researcher in Computational Biology at Karolinska Institute, Sweden 2022

Postdoctoral Researcher in Computational Biology is available for doctoral degree candidates in Bioinformatics, Computer science, Mathematics, Biostatistics, Neuroscience, or similar field at the Department of Clinical Neuroscience, Karolinska Institute, Sweden 2022 Qualification Details Qualified to be employed as a postdoctor is one who has obtained a doctorate or has equivalent…

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How to modify VCF file?

Hi community, I have a question: the SNP position in vcf file is from GRCh37/hg19, I need to change the position to GRCh38. So, I used UCSC liftover to replace the hg19 pos by GRCh38 pos and deleted some SNPs, then sorted the pos and saved to a new vcf…

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Table 5 | Scripting Analyses of Genomes in Ensembl Plants

arabidopsis_thaliana The 1001 Genomes Project [18] arabidopsis_thaliana Nordborg [19] brachypodium_distachyon Jaiswal_lab_OSU [20] hordeum_vulgare International Barley Sequencing Consortium (IBSC) [21,22,23] hordeum_vulgare Ensembl Plants [24] hordeum_vulgare Illumina iSelect SNP chip [22] malus_domestica fruitbreedomics.com [25] oryza_glaberrima Glab (OGE) oryza_glaberrima Barthii (OGE) oryza_glumipatula Oryza Genome Evolution (OGE) oryza_indica dbSNP [26] oryza_sativa www.ebi.ac.uk/eva [27,28,29,30] oryza_sativa…

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python – Matching two files(vcf to maf) using a dictionaries, and appending the contents

annotation_file ##INFO=<ID=ClinVar_CLNSIG,Number=.,xxx ##INFO=<ID=ClinVar_CLNREVSTAT,Number=.,yyy ##INFO=<ID=ClinVar_CLNDN,Number=.zzz #CHROM POS ID REF ALT QUAL FILTER INFO chr1 10145 . AAC A 101.83 . AC=2;AF=0.067;AN=30;aaa chr1 10146 . AC A 98.25 . AC=2;AF=0.083;AN=24;bbb chr1 10146 . AC * 79.25 . AC=2;AF=0.083;AN=24;ccc chr1 10439 . AC A 81.33 . AC=1;AF=0.008333;AN=120;ddd chr1 10450 . T G 53.09…

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08 compare visualization results of different annotation software

stay In the first two sections , We compared the differences vcf Use of annotation software , And convert the demerit recorded after the annotation into maf File format , because snpeff The comment result cannot be converted to maf, So we will compare later ANNOVAR、VEP、GATK Funcatator The results of…

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TwinEQTL: Ultra Fast and Powerful Association Analysis for eQTL and GWAS in Twin Studies

doi: 10.1093/genetics/iyac088. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA. 2 Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599, USA. 3 Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA. 4 Gilead…

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Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Arlinghaus, R. et al. Governing the recreational dimension of global fisheries. Proc. Nat. Acad. Sci. USA 116, 5209–5213 (2019). CAS  PubMed  PubMed Central  Article  Google Scholar  Cowx, I. G. & Gerdeaux, D. The effects of fisheries management practises on freshwater ecosystems. Fish. Manag. Ecol. 11, 145–151 (2004). Article  Google Scholar …

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS  PubMed  PubMed Central  Google Scholar  Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47,…

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how to predict gene expression from genotype file using already developed elastic net model

how to predict gene expression from genotype file using already developed elastic net model 0 Hello everyone, I want to predict gene expression from genotype file and already developed elastic net model. My model file look like this: GENE RSID1 RSID2 VALUE ENSG00000107937.18 rs7475652 rs7475652 0.531316876443232 ENSG00000107937.18 rs7475652 rs7918643 -0.1434806647803035…

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Help with PCA plot from SNPRelate

Hello, BioStars community! I am working on a datase of 50 samples(between cases and controls) with genotyping data for ~200 SNPs. I ran SNPRelate PCA analysis without adding population data and tried to plot its results. My PCA plot seems a bit “strange” since the observations did not come together…

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BAM file and no RNAME or POS information? : bioinformatics

Newbie here. Please, play nice. I got possession of a set of 4 .bam files that stores the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with…

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Dissertations.se: HETEROPLASMY

Showing result 1 – 5 of 7 swedish dissertations containing the word Heteroplasmy. Author : Guilherme Costa Baião; Lisa Klasson; Alistair Darby; Uppsala universitet; []Keywords : NATURAL SCIENCES; NATURVETENSKAP; NATURVETENSKAP; NATURAL SCIENCES; Wolbachia; Drosophila; Drosophila paulistorum; Differential Gene Expression; Reproductive Incompatibility; Reproductive Isolation; Comparative Genomics; Transcriptomics; RNA-Seq; Heteroplasmy; Mitochondria; Genomic…

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A Highly Sensitive and Specific Detection Method for Mycobacterium tuberculosis Fluoroquinolone Resistance Mutations Utilizing the CRISPR-Cas13a System

Objectives CRISPR-Cas13a system-based nucleic acid detection methods are reported to have rapid and sensitive DNA detection. However, the screening strategy for crRNAs that enables CRISPR-Cas13a single-base resolution DNA detection of human pathogens remains unclear. Methods A combined rational design and target mutation-anchoring CRISPR RNA (crRNA) screening strategy was proposed. Results…

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Mediation analysis of local chromatin state and gene expression data in human cell lines.

SNP associations with (a) SLFN5 and (b) GPR63 expression (top) and nearby chromatin accessibility (bottom) for variants on the genes’ chromosome. Peak SNPs are labeled. Mediation results for the (c) SLFN5 eQTL and (d) GPR63 eQTL. Log posterior odds from Bayesian model selection (top), -log10 p-values from Sobel test (middle),…

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difficulty filtering vcf file with vcftools

difficulty filtering vcf file with vcftools 1 I had a large VCF file named “common_known_variants.vcf ” which contains all known human variants downloaded from ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-common_all.vcf.gz -O common_known_variants.vcf.gz I’m trying to extract the known variants from only chromosomes 1,2,3,9,22, and X and write them in a new vcf file with the…

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Latest dbSNP VCF

This is the directory you’re looking for: ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/ curl -s ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.39.gz | zcat | head ##fileformat=VCFv4.2 ##fileDate=20210513 ##source=dbSNP ##dbSNP_BUILD_ID=155 ##reference=GRCh38.p13 ##phasing=partial ##INFO=<ID=RS,Number=1,Type=Integer,Description=”dbSNP ID (i.e. rs number)”> ##INFO=<ID=GENEINFO,Number=1,Type=String,Description=”Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a…

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Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

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Restriction Fragment Length Polymorphism – Top Future point

In molecular biology , restriction fragment length polymorphism ( RFLP ) is a technique that exploits variations in homologous DNA sequences, known as polymorphisms , in order to distinguish individuals, populations, or species or to indicate the locations of For in the gene within a sequence. The term may refer…

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Integrative analysis of eQTL and GWAS summary statistics reveals transcriptomic alteration in Alzheimer brains | BMC Medical Genomics

Significant gene-AD associations With the GWAS summary data from the IGAP and eQTL summary data from BRAINEAC, we performed both SMR and HEIDI tests to estimate the gene-AD associations in three human brain regions: frontal cortex, temporal cortex, and hippocampal regions. For the frontal cortex and hippocampal regions, we obtained…

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snp – Reference variant detected as altered one in bam file

I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer look to some calls. I found interesting, homozygous one rs477033 (C/G Ref/Alt) with flag ‘COMMON=0’ and very low MAF. I also…

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Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Cattle are among the largest populations of domesticated animals and used as food resources for humans; therefore, their phenotypes and genetic structure have been shaped by artificial selection for human needs and natural adaptation to environmental changes. The phenotypic selection causes genomic changes in breeding traits within breeds, resulting in…

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aCGH – Allie: Result by abbreviation

1  array comparative genomic hybridization(1473 times) Neoplasms(306 times) FISH (238 times)CNVs (135 times)MLPA (72 times) 2003 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. 2  array CGH(43 times) Neoplasms(12 times) CNVs (7 times)FISH (3 times)ID (3 times) 2003 Combined array comparative genomic hybridization and…

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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Bioconductor – Rsubread

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see Rsubread. Rsubread: high-performance read alignment, quantification and mutation discovery Bioconductor version: 2.13 This R package provides easy-to-use tools for analyzing next-gen sequencing read data. Functions of these tools include quality assessment, read alignment,…

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Polygenic Transcriptome Risk Scores for COPD Show Improved Cross-Ancestry Portability

NEW YORK — Polygenic transcriptome risk scores may be better at gauging chronic obstructive pulmonary disease susceptibility across human ancestry groups than polygenic risk scores, a new study has found. COPD affects about 16 million people in the US and is typically diagnosed through two measures of lung function: forced…

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wrong number of fields ?

Error occurence after merging files with bcftools: wrong number of fields ? 1 I have multiple vcf of CASES and CONTROLS variations annotated by VEP, SNPEff, SnpSift. first pair vcf -> only variations| CASES and CONTROLS second pair vcf -> variations + SnpEff | CASES and CONTROLS third pair vcf->…

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Solved based on the Manhattan plot of GWAS study looking at

Transcribed image text: Based on the Manhattan plot of GWAS study looking at alleles associated with breast cancer in a Japanese population (below). what can you conclude about the SNP rs 1177 (Choose the best answer.) GWAS of breast cancer in Japanese population 78117 60 5334 18366 r3589 are dortor…

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Genetic characteristics involving the PD-1/PD-L1/L2 and CD73/A2aR axes and the immunosuppressive microenvironment in DLBCL

Key messages What is already known on this topic Targeting immunosuppressive pathways have emerged as promising strategies for cancer treatment. The genetic characteristics of PD-1/PD-L1/L2 (programmed cell death protein 1/programmed cell death ligand 1/ligand 2) and CD73/A2aR (A2a adenosine receptor) and the effect of these two signalings on dysfunctional CD8+…

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Bioconductor – SNPRelate

DOI: 10.18129/B9.bioc.SNPRelate     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SNPRelate. Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data Bioconductor version: 3.12 Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and…

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How to Select data for a SNP for all samples using PLINK

How to Select data for a SNP for all samples using PLINK 0 Hello Folks, I’m very new to this plink. The below task has been assigned, any reference/blogs/Articles much appreciated. Q: Be able to select data for an SNP for all samples using PLINK please help plink • 49…

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Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Fricke, R., Eschmeyer, W. N. & van der Laan, R. (eds). Eschmeyer’s Catalog of Fishes: Genera, Species, Rererences. researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Electronic version, Accessed 15 October 2021. Nelson, J. S. Fishes of the World 4th edn, 372 (Wiley, 2006). Google Scholar  Chen, X. H., Lin, K. B. & Wang, X. W. Outbreaks…

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Untangling SNP Variations within CYP2D6 Gene in Croatian Roma

CYP2D6 is a highly polymorphic gene whose variations affect its enzyme activity. To assess whether the specific population history of Roma, characterized by constant migrations and endogamy, influenced the distribution of alleles and thus phenotypes, the CYP2D6 gene was sequenced using NGS (Next Generation Sequencing) method-targeted sequencing in three groups…

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rna seq – RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias

I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters. Aim We would like to conduct SNP discovery of these samples. Objective Our ultimate goal with this genotypic data is to search for variants (both SNPs and indels)…

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Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages

Díaz, S. et al. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES, 2019). Fisher, R. A. The correlation between relatives on the supposition of Mendelian inheritance. Earth Environ. Sci. Trans. R. Soc. Edinb. 52,…

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Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases

Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed  PubMed Central  Google Scholar  El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…

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Understanding signatures of positive natural selection in human zinc transporter genes

Datasets and populations We first compiled whole-genome sequencing data to analyze the patterns of variation in ZTGs on two geographical levels. Thus, we explored a worldwide dataset of 2,328 unrelated individuals representing 24 populations across Africa (AFR), Europe (EUR), East Asia (EAS), South Asia (SAS) and America (AMR), denoted as…

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Understanding the number of intersection in bedtools jaccard

Understanding the number of intersection in bedtools jaccard 1 Hello, I am using bedtools jaccard to compare two vcf files, as: bedtools jaccard -a ancestors.calls.norm.snp.vcf.gz -b GC078310.calls.norm.snp.vcf.gz intersection union-intersection jaccard n_intersections 1606899 1806667 0.889427 1536700 What I do not get is why n_intersections is equal to 1536700. Especially, the difference…

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R: PC gamma

PCgamma {GSAgm} R Documentation PC gamma Description For GSA of SNP data, the following two-step procedure is implemented (see Biernacka et al[1] for more details on the method). Step 1: Principal components analysis for SNPs within a gene is completed with the components needed to explain 80 percent of the…

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Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Vamosi, J. C., Magallon, S., Mayrose, I., Otto, S. P. & Sauquet, H. Macroevolutionary patterns of flowering plant speciation and extinction. Annu. Rev. Plant Biol. 69, 685–706 (2018). CAS  PubMed  Google Scholar  Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Syst. 27, 83–109 (1996)….

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rs532111960 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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CD Genomics: Bioinformatics-Analysis Division Provides Genotyping Analysis Service for Studying Genetic Variations

New York, USA – February 23, 2022 – The Bioinformatics-analysis division is a new division of CD Genomics that provides reliable next-generation and third-generation high-throughput sequencing data analysis, comprehensive technology services, database construction, and other related data analysis services. CD Genomics recently launched various types of genotyping analysis services, including…

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AutoKinship at GEDmatch by Genetic Affairs

Genetic Affairs has created a new version of AutoKinship at GEDmatch. The new AutoKinship report adds new features, allows for more kits to be included in the analysis, and integrates multiple reports together: AutoCluster – the autoclusters we all know and love AutoSegment – clusters based on segments AutoTree –…

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Phylogenomic analysis of CTX-M-15-producing Enterobacter hormaechei belonging to the high-risk ST78 from animal infection: Another successful One Health clone?

Available online 18 February 2022 doi.org/10.1016/j.jgar.2022.02.010Get rights and content Highlights • ESBL-positive Enterobacter cloacae complex members are critical priority pathogens. • E. hormaechei belonging to sequence type (ST) ST78 is an emergent high-risk clone. • Phylogenomic data of an E. hormaechei ST78/CTX-M-15 infecting a calf is presented. • E. hormaechei…

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EQTL visualization

EQTL visualization 0 I have generated file from MATRIXEQTL . I would like to visualize haploblocks, plots for MATRIXEQTL. I am having SNP.txt, Gene expression.txt. How can I visualize Chromosome specific eQTL list EQTL plot • 53 views • link 17 hours ago by Nai &utrif; 20 Login before adding…

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Genomic analysis on Galaxy using Azure CycleCloud

Cloud computing and digital transformation have been powerful enablers for genomics. Genomics is expected to be an exabase-scale big data domain by 2025, posing data acquisition and storage challenges on par with other major generators of big data. Embracing digital transformation offers a practically limitless ability to meet the genomic…

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PostDoc Plant Bioinformatics job with SKOLKOVO INSTITUTE OF SCIENCE AND TECHNOLOGY

<p><strong>Want to participate to the outstanding new area of agro-genomics ? To put into the practice how the genetic diversity and genome-assisted breeding in crops contribute to provide healthy and high quality food in a sustainable way to humankind? Strong in bioinformatics and interested in working with very large datasets…

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A core genome MLST (cgMLST) scheme for Mycobacterium abscessus complex subspecies

Dataset for manuscript “The use of comparative genomic analysis for the development of subspecies-specific PCR assays for the Mycobacterium abscessus complex” by Winifred Akwani et al. A core genome MLST scheme was developed for Mycobacterium abscessus complex (MABC) subspecies M. abscessus, M. bolletii and M. massiliense, using chewBBACA version 2.8.5…

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snp.plotter_ input files

snp.plotter_ input files 0 Dear friends I’m running an LD analysis using the package of snp.plotter in R The problem that I’m facing right now is the files that I need to use for running the analysis My first question is why there is no template for the config.file??? what…

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dbSNP – Wikipedia @ WordDisk

The Single Nucleotide Polymorphism Database[1] (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Although the name of the database implies a collection of…

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rs9789283 RefSNP Report – dbSNP

Help Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When…

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Frontiers | Association of Maternal Dietary Habits and MTHFD1 Gene Polymorphisms With Ventricular Septal Defects in Offspring: A Case-Control Study

Introduction Congenital heart disease (CHD) refers to a group of anatomic heart and great vessel malformations that arise during the embryologic development of the fetus. CHD is one of the most prevalent birth defects, affecting around 2.50 out of every 1,000 births in China (1), and it imposes a substantial…

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qctool to merge two bgen file fails with no clear reason to

Hi, I am trying to merge two bgen files using qctool as explained here. I am using qctool_v2.2.0. The command works but ends with an error: ❱ qctool -g bug/in2.bgen -s bug/in2.sample -merge-in bug/in1.bgen bug/in1.sample -og bla.bgen -os bla.sample Welcome to qctool (version: 2.2.0, revision: unknown) (C) 2009-2020 University of…

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GATK HaplotypeCaller with interval list

I am trying to use the -L option of GATK HaplotypeCaller to call SNPs and short InDels with in an interval list. My interval list file (top8snp.interval_list) content is as follows: 12 33029845 33030845 + rs24767598 13 40586682 40587682 + rs24748362 18 24373857 24374857 + rs8856159 21 50381146 50382146 +…

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Active Motif Incorporated Announces the Acquisition of Amaryllis Nucleics and their proprietary RNASeq workflow

CARLSBAD, Calif., Jan. 27, 2022 /PRNewswire/ — Active Motif Incorporated, a company with the vision of bringing epigenetics more deeply into precision medicine, announced that it has purchased Amaryllis Nucleics, a Bay Area-based start-up company focused on proprietary RNA Sequencing methods. Amaryllis Nucleics provides Active Motif with a streamlined, low-cost…

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DNA Labs International Launches the Newest Technology for Forensic Genetic Genealogy

MiSeq FGx platform by Verogen DEERFIELD BEACH, Fla. (PRWEB) January 26, 2022 DNA Labs International, which specializes in forensic DNA analysis including forensic genetic genealogy (FGG) for law enforcement agencies, government forensic labs, and attorneys, is announcing the release of their newest technology, Single Nucleotide Polymorphism (SNP) testing with…

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To use rflp analysis to detect a snp. the snp must _______.

To use RFLP analysis to detect a single nucleotide polymorphism (i.e., a SNP), the SNP must _______. To use RFLP analysis to detect a single nucleotide polymorphism (i.e., a SNP), the SNP must _______. cause disease occur in homozygous form occur within a restriction enzyme recognition sequence be present in…

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Download full list of SNPs and their coordinates in hg38

Download full list of SNPs and their coordinates in hg38 3 What is the best / standard place to get a full list of SNPs and their coordinates in hg38? I downloaded the SNPsnap database, but just realized that those coordinates are in hg19. I’m trying to figure out how…

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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The Genetic Architecture of Sleep Health Scores in the UK

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

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High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets

Abstract The antisense non-coding RNA in the INK locus (ANRIL) is a hotspot for genetic variants associated with cardiometabolic disease. We recently found increased ANRIL abundance in human pancreatic islets from donors with certain Type II Diabetes (T2D) risk-SNPs, including a T2D risk-SNP located within ANRIL exon 2 associated with…

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Do we need to apply the same p-value threshold on all 22 chromsomes?

Polygenic Risk Score Calculation: Do we need to apply the same p-value threshold on all 22 chromsomes? 1 Hi there, I am using PRSice-2 to calculate the polygenic risk score for 22 chromosomes one by one. To my understanding, since the 22 chromosomes are independent of each other, and our…

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Toll-like receptor 2/4 in Chinese patients with sepsis

Introduction Sepsis is a life-threatening organ dysfunction that results from an exaggerated host immune response to disseminate infection.1 Despite improvements in treatment strategies, sepsis remains a leading cause of death in critically ill patients worldwide.2 Low platelet number, known as thrombocytopenia, is common in infectious diseases (also sometimes referred to…

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bedtools intersect error: Invalid record in file

Hello to all I am trying to run bedtools intersect with vcf file and a bed file (my goal is to add the depth data to my VCF) I get an error running this command: bedtools intersect -a depth.bed -b fish.vcf -wa -wb > $out The error: “Error: Invalid record…

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What is SNP array testing?

What is SNP array testing? The SNP array test looks for changes in specific areas of a person’s chromosomes, such as gains (duplications) or losses (deletions). These gains or losses result in extra or missing copies of genetic material. How does SNP array work? SNP array is a type of…

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Associate Scientist, Bioinformatics – jobRxiv

Are you interested in being a key member of a bioinformatics team in a shared resource at a major cancer center?  This Associate Scientist position will support a wide array of bioinformatics research services in the Sylvester Comprehensive Cancer Center (SCCC) Biostatistics and Bioinformatics Shared Resource (BBSR) at the University…

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SNP associated contigs

SNP associated contigs 0 I am using usegalaxy.org for SNP analysis. After mapping with bowtie2 I got BAM file including QNAME FLAG RNAME POS and on variant calling I got Chrom Pos ID Ref Alt. Showing Variant position on reference genome. I want to get those sequences associated to SNP….

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Bioinformatics, Computer Science, Biology – Transcriptomic, Genomic Assays (f/m/d) – Evotec International GmbH – Biologie & Life Sciences

Evotec is a life science company with a unique business model focused on delivering highly effective new therapeutics to the patients. The Company leverages its multimodality platform, the “Data-driven R&D Autobahn to Cures”, for proprietary projects and within a network of partners including Pharma, Biotech, academics, and other healthcare stakeholders….

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Variant physical position must be monotonically increasing

ERROR: Variant physical position must be monotonically increasing 0 I want to calculate XPEHH for each SNP position. When I run the following command selscan –xpehh –vcf B10_beagle.vcf –vcf-ref D6_beagle.vcf –map MAP.map –threads 8 –out B10vsD6 I get this error ERROR: Variant physical position must be monotonically increasing Ch2:66 66…

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Cytogenomic Molecular Inversion Probe Array FFPE Tissue – Products of Conception

Cytogenetic Test Request Form Recommended (ARUP form #43098) Ordering Recommendation Recommendations when to order or not order the test. May include related or preferred tests. Use to detect copy number alterations and loss of heterozygosity in FFPE specimens from products of conception. Mnemonic Unique test identifier. CMAPFFPE Methodology Process(es) used…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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17q12-21 risk-variants influence cord blood immune regulation and multitrigger-wheeze

Background: Childhood wheeze represents a first symptom of asthma. Early identification of children at risk for wheeze related to 17q12-21 variants and their underlying immunological mechanisms remain unknown. We aimed to assess the influence of 17q12-21 variants and mRNA-expression at birth on development of wheeze. Methods: Children were classified as…

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Very important pharmacogene variants in the Blang population

Introduction The use of drugs should be different among diverse ethnic groups because of differences in ethnicity, age, sex, environmental factors and genetic factors. If these differences are ignored, then drug sensitivity, metabolic rate, and adverse reactions are affected, which influences the curative effect of drugs and aggravates the illness…

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How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice

How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice 1 This is a two part question. First, when implementing PRSice, is there a way to make sure certain SNPs are retained for the PRS calculation? I basically want to avoid…

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Bioconductor Tools for Microarray Data Analysis

References ………………………………………………………………………………………..478 17.1 INTRODUCTION 17.1.1 WHAT IS BIOCONDUCTOR? Bioconductor [1] is an open source software project for the R statistical computing language. The main aim of the project is to provide R packages to facilitate the analysis of DNA microarray, sequencing, SNP and other genomic data. In addition for data,…

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Reference panel data to be used for GCTA-COJO

Reference panel data to be used for GCTA-COJO 0 I performed a genome-wide meta-analysis based on summary statistics from the four cohorts to identify significant loci. Next, I would like to perform a conditional analysis using GCTA-COJO to search for SNPs independent of significant lead SNPs. I know that GCTA…

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Blast command line pipeline not working

Blast command line pipeline not working 0 Hello, I am running now a local blast pipeline using MacOs. The goal here is to take interval of the 5 best hits and then extract the SNP variants from multiple vcf.gz files. But I am facing an error which I cannot solve….

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Padding out a GVCF file with 1000G exomes to get gatk VariantRecalibrator working with a small sample

I’ve got sequencing data for a small 500 bp amplicon from a few samples. GATK best principles suggest running VariantRecalibrator on the GVCF files I generate. I’m trying to get this working, but I get an error about “Found annotations with zero variances”. Reading the gatk manual and other posts…

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Natera launches Prospera with quantification to improve kidney graft rejection testing

Natera has announced the launch of Prospera with quantification, the only cell-free DNA (cfDNA) test for kidney rejection that provides three values—the quantity of donor-derived cfDNA (dd-cfDNA), fraction of dd-cfDNA, and total cfDNA—on every report. Combining these three metrics has been shown to improve sensitivity when evaluating transplant rejection, compared…

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Mitochondrial DNA-like sequences in the human nuclear genome: Characterization and implications in the evolution of mitochondrial DNA

The complete mitochondrial genome of Flustrellidra hispida (Bryozoa, Ctenostomata, Flustrellidridae) was sequenced using a transposon-mediated approach. All but one of the 36 genes were identified (trnS2). The genome is 13,026 bp long, being one of the smallest metazoan mitochondrial genomes sequenced to date with a unique gene order when compared to…

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PLINK sanity check – Bioinformatics Stack Exchange

I am a new user of PLINK and am analysing some SNP data for the first time. After creating a .bim file with $ plink –file my_data –make-bed I notice that for several SNPs my data is different from dbSNP e.g. rs145496306: BIM file: A G dbSNP: G>A,T rs3813199: BIM…

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Large-scale genome-wide study reveals climate adaptive variability in a cosmopolitan pest

Genomic data The foundational resource for this study was a dataset of 40,107,925 nuclear SNPs sequenced from a worldwide sample of 532 DBM individuals collected in 114 different sites based on our previous project15. DNA was extracted from each of the 532 individuals using DNeasy Blood and Tissue Kit (Qiagen,…

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SNP extraction

SNP extraction 0 I want to extract specific SNPs of interest i have in a text file into an additive genetics model so that each SNP can be in a 0/1/2 format for each subject using genetics info in from PLINK (.bed, .bim, and .fam files). How can i do…

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gatk VariantRecalibrator positional argument error

I’m trying to use recalibrate my vcf using gatk VariantRecalibrator, but keep getting an error “Illegal argument value: Positional arguments were provided”. But I don’t know what this means, or how to correct it! Here’s my call: gatk VariantRecalibrator -R “/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/Homo_sapiens_assembly38.fasta” -V “$OUT”/results/variants/”$SN”.norm.vcf.gz -AS –resource hapmap,known=false,training=true,truth=true,prior=15.0: “/Volumes/Seagate…

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No quality in non-variant sites GATK

No quality in non-variant sites GATK 1 Heys, I am doing the SNP calling with Haplotypecaller BP_Resolution, CombineGVCFs with convert-to-base-pair-resolution and GenotypeGVCFs with include-non-variant-sites with GATK and when I get my vcf file, the non-variant sites does not have any quality at all: #CHROM POS ID REF ALT QUAL FILTER…

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Removing contamination with SNP tools

Removing contamination with SNP tools 0 Hello everyone, Currently, I’m working on a ChIPseq dataset where I will analyze chromatin marks on transposons and genes in a fungus. Unfortunately, I got some contamination in my data from a closely related species. Because they are so similar, removing contamination based on…

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New bioinformatics tool spots hybrid fish that threaten survival of natural tilapia populations in aquaculture

A new genomics marker tool has been shown to accurately identify tilapia species and tell apart their hybrids, providing a novel resource to help develop aquaculture and empower conservation in Tanzania, Africa. Crucially, the new tool offers a cheaper solution than full genome data analysis — the current approach to…

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What is the single nucleotide polymorphism database ( dbsnp )?

The Single Nucleotide Polymorphism Database (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Furthermore, are there any databases for single nucleotide polymorphisms?As there…

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SNP2TFBS

SNP2TFBS Viewing variants that affect TF binding – Results – SNP identifier Chrom id (Feb 2009 GRCh37/hg19) SNP position NB. of TF factors rs1800629   dbSNP NC_000006.11 (chr6) 31543031 1 TF name  PWM score on Ref PWM score on Alt Score difference Low Score Thr High Score Thr MZF1_1-4  1024  ….

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Ethnic Diversity of DPD activity and the DPYD Gene

Plain Language Summary Fluoropyrimidine (FP; 5-FU, capecitabine) is a common chemotherapy used to treat many different cancers, including cancer of the colon and rectum, upper digestive tract, breast and head and neck. Cancer patients who receive FP chemotherapy are at risk of developing severe side effects from their treatment. A…

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the spacer of sgrna will hybridize with this sequence of dna from the fragment shown below?

James Guys, does anyone know the answer? get the spacer of sgrna will hybridize with this sequence of dna from the fragment shown below? from EN Bilgi. Solved The spacer of sgRNA will hybridize with this sequence Answer to Solved The spacer of sgRNA will hybridize with this sequence Do…

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Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands Wouter van Rheenen, Rick A. A. van der Spek, Mark K. Bakker, Joke J. F. A. van Vugt, Paul J. Hop, Ramona A. J. Zwamborn, Annelot M. Dekker, Klara Gawor, Henk-Jan Westeneng, Gijs H. P. Tazelaar, Kristel R. van Eijk, Maarten Kooyman, Ewout J. N. Groen, Michael…

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Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

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One-hot encoding for PLINK or VCF

One-hot encoding for PLINK or VCF 0 I want to write an autoencoder for SNP data. Is there an established way to one-hot-encode binary PLINK or VCF input? I believe that can be done by manipulating PLINK’s bed file but am afraid to do something wrong. By one-hot encoding I…

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GitHub – AI-sandbox/gnomix

This repository includes a python implemenation of Gnomix, a fast and accurate local ancestry method. Gnomix can be used in two ways: training a model from scratch using reference training data or loading a pre-trained Gnomix model (see Pre-Trained Models below) In both cases the models are used to infer…

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Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis

Global phylogenetic analysis A Maximum Likelihood (ML) phylogenetic tree based on the 69 M. bovis isolates and reference genome was obtained (Fig. 2A). This strategy allows the generation of a more robust tree, when comparing with single gene based trees or multi-locus based trees, that do not capture the variability across the…

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Problem with viewing BAM files in IGV

Problem with viewing BAM files in IGV 1 Hi everyone, I’m quite new to bioinformatics and I’m having some beginner problems with IGV. I’ve got some BAM files that were generated using the GATK best practice pipeline for SNP discovery, with BAI files located in the same directory. I’m using…

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Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs

Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs 0 I have a set of 58000 SNPs for which the SNP ID is in the format of: chr:pos:effect allele:ref allele (Grch37 build), but I need to convert this to rsID where one is available for the SNP. I’ve tried using…

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vcf to bgen conversion using qctool v2 yields 0 snps

Hi all, I have a vcf file that was extracted from UKB data using qctool (v2.0.6-Ubuntu16.04-x86_64) and contains data in the GP format. This contains a bunch of SNPs from a single chromosome. ❱ wc -l chromosome1.vcf 260 chromosome1.vcf Then I try to convert this file to .bgen again using…

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