Category: VEP

vcf – Ensembl Variant Effect Predictor (VEP) issue during execution

vcf – Ensembl Variant Effect Predictor (VEP) issue during execution – Bioinformatics Stack Exchange …

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Using VEP to get gnomAD frequencies

Hi all, I am using Ensembl VEP (command line) to annotate a VCF I have. I am specifically looking for gnomAD allele frequencies, which is fairly straight forward to do, technically speaking. However, the data looks off in some cases. For example, when I pass in: 10 69408929 COSM3751912 A…

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Using VEP to get gnomAD frequencies

Hi all, I am using Ensembl VEP (command line) to annotate a VCF I have. I am specifically looking for gnomAD allele frequencies, which is fairly straight forward to do, technically speaking. However, the data looks off in some cases. For example, when I pass in: 10 69408929 COSM3751912 A…

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Ensembl FTP Mirror in USA? Slow Downloads

Ensembl FTP Mirror in USA? Slow Downloads 1 Hello I work on a fairly good cluster at an R1 university in the USA. I am downloading the VEP 101 indexed cache files and it’s slow as Christmas. I mean AOL speeds slow. If I download a similar size file from…

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Ensembl FTP Mirror in USA? Slow Downloads

Ensembl FTP Mirror in USA? Slow Downloads 1 Hello I work on a fairly good cluster at an R1 university in the USA. I am downloading the VEP 101 indexed cache files and it’s slow as Christmas. I mean AOL speeds slow. If I download a similar size file from…

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Best tool for genotype – phenotype correlation

Best tool for genotype – phenotype correlation 0 Hello, I need to perform genotype – phenotype correlation analysis. I know PLINK could be used for such purpose, but with PLINK many file preparation steps need to be done before running the actual step. I have VEP annotated VCFs. Maybe other…

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categorizing VEP annotations into consequences

categorizing VEP annotations into consequences 1 Hello, I need to run downstream analysis where counts of functional and synonymous variants are needed. I have VCFs annotated with VEP. When annotating variants with VEP, in is not quite understandable, which outputs could be counted as synonymous and functional. It is, of…

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Bioinformatics Analyst II – Remote at Geisinger Health System

Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research. Performs and supervises complex data extraction, transformation, visualization, and summarization to support Research…

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“Given ref” field is empty when a ref. allele was in VCF input

VEP: “Given ref” field is empty when a ref. allele was in VCF input 0 Hi there, I’m running VEP using the following command: ref=”GRCh38.primary_assembly.genome.fa” vep=”/opt/vep_ensembl/ensembl-vep/vep” for ea in *Somatic.hc.vcf do $vep -i $ea -o vep/”$(echo $ea | sed s/.vcf//)”_VEP.txt –cache –dir_cache “/home/shared/vep_cache/” –assembly GRCh38 –merged –fasta $ref –hgvs –hgvsg…

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How to annotate SNVs in a BAC sequenced by NGS

Hello, I’m trying to annotate variations in NGS data from bacterial artificial chromosomes with respect to the reference sequence. To do this i build a map of the BAC (including vector) and map the NGS reads to this BAC map. I also use a variant caller to find any differences…

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annotating vcf with variant type and variant effect, and most harmful effect

annotating vcf with variant type and variant effect, and most harmful effect 0 Hello, I have a VCF with ~6000 variants. The build is GRCh37. I want to annotate each variant with its type (substitution, deletion, inversion) and its effect (missense, silent, intergenic). If there are competing or multiple effects,…

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Factors influencing multidrug-resistant tuberculosis | IDR

Introduction Pediatric tuberculosis (TB) is a significant global health threat and is one of the top ten causes of death in children.1 Globally, in 2019, an estimated 10.0 million people fell ill with TB, with children (aged under 15 years old) accounting for 12%, causing 1.4 million deaths.2 With the…

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PER1 as a Tumor Suppressor Attenuates Breast Cancer

Introduction Breast cancer is one of the most common malignancies in women, with a high mortality rate around the world.1,2 Although multidisciplinary therapeutic strategies, including surgical resection, chemoradiotherapy, endocrine and anti-HER2 therapy, have made substantial progress over the past decade, there are still a considerable proportion of breast cancer patients…

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Synchronous rectal tumours in a patient with Lynch syndrome

Plain Language Summary The increasingly widespread use of immunohistochemistry and next-generation sequencing in the detection of microsatellite instability (MSI) and DNA mismatch repair (MMR) status has led to the observation of various unusual tumour types that exhibit MMR protein deficiency in Lynch syndrome. Here, we report a case of two…

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Severe trauma and burns accompanied by sepsis

Introduction Trauma accounts for approximately 10% of deaths and 16% of disabilities worldwide.1 Billions of dollars have been spent on research into new biological therapeutics for severe injuries, as well as post-traumatic sepsis and septic shock.2 Burn injuries cause unpredictable trauma and sepsis is a complication associated with high morbidity…

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Periprosthetic joint infection caused by Mycoplasma hominis

Introduction Total knee arthroplasty (TKA) is a common and effective orthopedic procedure to treat severe osteoarthritis and rheumatoid arthritis.1 Periprosthetic joint infection(PJI) proves to be a serious complication following TKA.2 Although the overall incidence of PJI is low at 0.5–2.0% after primary TKA, it still brings a large burden on…

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Atherosclerosis Pathways are Activated in Pericoronary Adipose Tissue

Introduction Obesity, particularly abdominal obesity, is one of the most important risk factors for atherosclerosis and cardiovascular events.1–3 The volume and thickness of epicardial adipose tissue (EAT) correlate with intra-abdominal fat mass and the severity of obesity4,5 and are independently associated with cardiovascular events.6 Many studies have shown that inflammation…

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Sequencing for pulmonary fungal infection diagnosis

Introduction In recent years, with the increase in high-risk groups requiring immunosuppressant use, the prevalence of pulmonary fungal disease has shown a significant upward trend. The main sources of fungal infections in human lungs are opportunistic fungi: Aspergillus, Cryptococcus, Pneumocystis jirovecii, and endemic fungi. Among them, Aspergillus and Cryptococcus are…

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Clinical Impact of X-Ray Repair Cross-Complementary 1 (XRCC1) and the

Plain Language Summary Colorectal cancer progresses through a well‑defined series of transformations from normal colonic epithelial cells to precursor adenoma lesions that eventually evolve into increasingly more invasive and malignant stages. An improved understanding of the genetic and molecular drivers of colorectal cancer, especially the progression of adenoma to carcinoma,…

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Seroprevalence of Hepatitis B Virus and Associated Factors Among Femal

Introduction Hepatitis B virus (HBV) is a DNA virus belonging to the Hepadnaviridae family.1,2 Despite the availability of a safe and effective vaccine against hepatitis B infection for over two decades now, the overall burden of the disease remains enormous with over 2 billion people infected worldwide and approximately 1…

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(2Z)-3-hydroxy-3-(4-R-phenyl)-prop-2-enedithioic acids | IDR

Introduction Mycobacterium tuberculosis is a pathogenic bacterium that is well known to be the causative agent of tuberculosis. The World Health Organization (WHO) has pinpointed this pathogen as one of the two leading causes worldwide of higher mortality resulting from an infectious agent. The increase in the number of cases…

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Cathie Wood’s Top 15 Small-Cap Stock Picks

In this article, we discuss Cathie Wood’s top 15 small-cap stock picks. If you want to skip our detailed analysis of Wood’s history, investment philosophy, and hedge fund performance, go directly to Cathie Wood’s Top 5 Small-Cap Stock Picks. Catherine Wood is an American millionaire investor, who founded ARK Investment…

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VEP allele frequency from gnomAD genomes

VEP allele frequency from gnomAD genomes 1 Hi, Biostars community. According to VEP documentation, gnomAD genomes database could be used with –custom option. Example from VEP dosc: ./vep -i examples/homo_sapiens_GRCh38.vcf –cache –custom gnomad.genomes.r2.0.1.sites.GRCh38.noVEP.vcf.gz,gnomADg,vcf,exact,0,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH But there is no gnomAD genomes file for all chromosomes on ensembl’s ftp source: ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/gnomad/r2.1/genomes/ Only data…

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The Profile and Function of Gut Microbiota in Diabetic Nephropathy

Introduction Diabetic nephropathy (DN) is characterized by kidney function loss caused by diabetes mellitus.1 Almost one-third of patients with diabetes have DN, and the prevalence of DN is increasing worldwide.2 DN is one of the most important factors of chronic kidney disease and end-stage renal disease (ESRD). The signs and…

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Sort a sub column within a column while keeping the feature (LINUX)

I have a vcf file with these column headers: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BS_25YES2E3 BS_G5B6AD28 BS_QCGPE1ZX A sample feature within that vcf file chr1 10450 . T C 27.94 VQSRTrancheSNP99.90to100.00+ AC=1;AF=0.167;AN=6;BaseQRankSum=-1.676e+00;ClippingRankSum=0.789;DP=102;ExcessHet=4.7712;FS=4.868;MLEAC=1;MLEAF=0.167;MQ=34.67;MQRankSum=-1.084e+00;PG=0,0,0;QD=1.55;ReadPosRankSum=-2.169e+00;SOR=0.707;VQSLOD=-1.050e+01;culprit=MQ;ANN=C|upstream_gene_variant|MODIFIER|**DDX11L1**|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1560|1||SNV|HGNC|HGNC:37102||||chr1:g.10450T>C,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1419|1||SNV|HGNC|HGNC:37102|YES|||chr1:g.10450T>C,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3954|-1||SNV|HGNC|HGNC:38034|YES|||chr1:g.10450T>C GT:AD:DP:FT:GQ:JL:JP:PL:PP 0/0:28,0:28:lowGQ:0:1:1:0,0,663:0,0,666 0/1:13,5:18:PASS:35:1:1:34,0,342:35,0,345 0/0:44,0:44:lowGQ:0:1:1:0,0,802:0,0,805 The portion in bold is what I want (DDX11L1). I…

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adding allele frequencies to a vcf

adding allele frequencies to a vcf 1 Hi all, I have a vcf file generated from a few hundred samples. For each variant within the file, I would like to calculate the allele frequency of each allele and then add that information as a field into the ‘INFO’ field of…

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VEP for cancer annotation using COSMIC

VEP for cancer annotation using COSMIC 2 Dear all, I’m struggling in finding how to obtain information about COSMIC database after I annotate a vcf using VEP. The command that I used is: vep -i Mutect2_unfiltered_10643_vs_2434.vcf.gz -o Mutect2_unfiltered_10643_vs_2434_VEP.ann.vcf –assembly GRCh38 –species homo_sapiens –offline –cache –cache_version 99 –dir_cache /.vep –everything –filter_common…

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VEP cache issues

VEP cache issues 1 Hello, need some help with VEP cache files. So, I downloaded cache file as written in this manual with www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache with curl -O ftp.ensembl.org/pub/release-102/variation/vep/homo_sapiens_vep_102_GRCh38.tar.gz I have file homo_sapiens_vep_102_GRCh38.tar.gz in my /.vep directory However, when running script, I got the error ——————– EXCEPTION ——————– MSG: ERROR: Cache…

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Extract variant consequence count from gnomad and patient VCF file

Hello, I have 2 types of VEP annotated VCF file – regular vcf and gnomad genome file. I would like to extract counts of both missense, synonymous, upstream and intron variants for each gene in each file. Output should be something similar to this: MHTFR: missense 23, intron 100, synonymous…

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FGFR2 inhibitors in intrahepatic cholangiocarcinoma

Massimiliano Salati,1,2 Francesco Caputo,1 Cinzia Baldessari,1 Pietro Carotenuto,3 Marco Messina,4 Stefania Caramaschi,5 Massimo Dominici,1 Luca Reggiani Bonetti5 1Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy; 2PhD Program Clinical and Experimental Medicine, University of Modena and Reggio Emilia, Modena, Italy; 3Department of Genomics, Telethon Institute of Genetics and…

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Genetic Factors Affecting Precision Pain Medicine

Introduction The overarching definition of precision pain medicine is that diagnosis and treatment can be customized to an individual’s specific risk profile.1,2 At its most basic, the ideology is based on using all available patient-level data to target therapies for that individual with regard to prediction, prevention, diagnosis, and treatment…

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Livingston Co. Sheriff’s Office investigating theft from county road department garage

LIVINGSTON COUNTY, Ky. (KFVS) – The sheriff’s office is investigating a theft from the county road department garage. According to deputies, between 7:30 p.m. on October 4 and 5:30 a.m. on Oct. 5, someone broke into the storage yard at the Livingston County Road Department garage. They said a white…

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Ensembl vep. How to filter population frequency less than 1%?

Ensembl vep. How to filter population frequency less than 1%? 0 Hi everyone, I have gotten many responses from the site even though I never asked a question, this is my first query. I am working with ensemble vep to annotate and filter a vcf file. With this script I…

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TNSKP in a Chinese tertiary hospital

Introduction Klebsiella pneumoniae belongs to the Enterobacteriaceae family and is an opportunistic pathogen that can transfer to multi-drug resistant strains and can cause various infections, including bacteremia, pneumonia, liver abscess, and urinary tract infection.1,2 At present, the spread of multi-drug resistant K. pneumoniae strains is a worldwide problem, and especially…

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Quantitative PCR assay for detection of Helicobacter pylori

Introduction Helicobacter pylori is a common pathogen that infects nearly 50% of the global population.1 Infection with this pathogen causes chronic gastritis, which can cause chronic gastroduodenal diseases such as gastritis, gastric ulcer, duodenal ulcer, gastric cancer, and gastric mucosa-associated lymphoid tissue (MALT) B-cell lymphoma.2 Although H. pylori is the…

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rpoB mutations and effects on rifampin resistance

Introduction Although the incidence and mortality rates of tuberculosis (TB) are slowly declining, TB is still a major global public health threat with reports of ~10 million new cases and 1.2 million deaths annually.1 In recent years, there has been an alarming increase in drug-resistant TB, which poses a serious…

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How do I get GO term annotations using VEP?

How do I get GO term annotations using VEP? 1 I’m running VEP version 85 in offline mode, but I wasn’t asked to download any database for GO. I’m using the GO.pm plugin in my command-line, but the GO column is completely empty. The Clinvar column is not empty, and…

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Vep : MNP phased genotype

Vep : MNP phased genotype 0 Hello all, I would like to know what is the best way to annotate a vcf taking into account the mnp. I specify that it is about a vcf with phased genotype. For annotations i used ensembl vep. I saw that there is in…

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Mutational profile of the dystrophin gene

Introduction Duchenne Muscular Dystrophy (DMD-OMIM #310200) and Becker Muscular Dystrophy (BMD-OMIM #300376), are the most common hereditary muscular dystrophies around the world.1 DMD and BMD occur with a frequency of 1/3.300 and 1/6.000 newborn males, respectively.2 These dystrophinopathies are caused by alterations in the DMD gene and have an X-linked…

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Vero cell-adapted Infectious Bursal Disease virus LC-75

Introduction Infectious bursal disease (IBD), also known as Gumboro, is an immunosuppressive disease of chickens and is the second priority chicken disease in Ethiopia, next to Newcastle disease, that needs to be controlled primarily through vaccination.1 The etiological agent is IBD virus (IBDV) which belongs to the family Birnaviridae, a…

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entry level bioinformatics jobs near me

Indeed ranks Job Ads based on a combination of employer bids and relevance, such as your search terms and other activity on Indeed. computer science, information science, Candidates should be interested in innovative, interdisciplinary approaches to modeling mammalian physiology and disease using approaches in data science,…. Sign up with Facebook….

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Job vacancy in Global Worldwide: Bioinformatics Analyst II – Remote at Geisinger

Job details Job type full-time Full job description Job summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from mycode community health initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health researchPerforms and supervises complex data extraction,…

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VEP: MSG: ERROR: Cannot use format vcf without Bio::DB::HTS::Tabix module installed

VEP: MSG: ERROR: Cannot use format vcf without Bio::DB::HTS::Tabix module installed 0 Hello everybody, I want to annotate a VCF file with vep (v. 104). I installed VEP and everything works fine. However, when using the –custom flag and a gnomAD.vcf file to annotate allele frequencies, I get the following…

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Multidrug-resistant Tuberculosis Strains in Southeast China

Introduction Multidrug-resistant TB (MDR-TB) infections, which result from transmission of Mycobacterium tuberculosis (MTB) strains with resistance to both rifampicin (RIF) and isoniazid (INH), continue to occur and are a major global public health issue. In 2019 an estimated 362,700 MDR-TB cases were detected worldwide, of which only 56.8% were properly…

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rs2507799 was found to be linked with increased risk for IS

Introduction Ischemic stroke (IS) is caused by the sudden loss of blood circulation to an area of the brain that causes injury to neurological function and represents a major cause of global disability and mortality.1 IS is known to be a heterogeneous and multifactorial disease. Genetic factors, particularly those involving…

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Ensembl phylogenetic context

Ensembl phylogenetic context 0 Hi, I was wondering if there is a way to download or generate 24 primates EPO-Extended alignments for a set of SNPs using Ensembl VEP. I can download it from the phylogenetic context section in Ensembl for a given SNP, but was wondering how to do…

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Identification of a Novel SLC8A1-ALK Fusion

Xingyu Zhu,1,* Yuqi He,2,* Yin Wang,3,* Yan Lei,3 Xiaoxing Su,3 Yifan Liu,1 Shuangxiu Wu,3 Zhengfu He1 1Department of Thoracic Surgery, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China; 2Monash School of Medicine, Monash University, Clayton, VIC, 3800, Australia; 3Berry Oncology Corporation, Beijing, 102206,…

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Bioconductor – ensemblVEP

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see ensemblVEP. R Interface to Ensembl Variant Effect Predictor Bioconductor version: 3.0 Query the Ensembl Variant Effect Predictor via the perl API Author: Valerie Obenchain <vobencha at fhcrc.org>, Maintainer: Valerie Obenchain <vobencha at fhcrc.org>…

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How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?

How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor? 0 I have multiple .vcf files for individuals (also have merged.vcf with all indivs.). I would like to predict each variants effect and then count variants with, e.g. IMPACT=HIGH. Is…

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Issues installing vep

Issues installing vep 0 I am having issues with installing ensembl’s vep on the HPC. It requires perl dependencies which I have successfully installed most of via anaconda. However I get the following error message when trying to run perl INSTALL.pl: Can’t locate Module/Build.pm in @INC (you may need to…

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Bioinformatics Analyst II – Remote job in Danville at Geisinger

Job Title Bioinformatics Analyst II – Remote Location Work from Home Job Category Information Technology Support Services Schedule Days Work Type Full time Department Research Informatics Department Date posted 09/22/2021 Job ID R-15599 Job Summary Primary accountability is to leverage the organization’s…

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Genotype distribution and prevalence of human papillomavirus

Introduction Cervical cancer (CC) is the second most deadly disease among women in the world and is the leading cause of death from cancer.1 In 2018, there were 570,000 new diseases and 311,000 deaths worldwide.2 Viral infections contribute to 15–20% of all cancers, and several viruses play an important role…

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Alamut batch vs free annotation tools like VEP

Alamut batch vs free annotation tools like VEP 1 Hello all, we are considering purchasing an alamut batch license for variant annotation. I would like to have your opinion knowing that it is very expensive, I wonder what it really brings compared to VEP (with the use of plugin to…

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miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

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hypothetical protein DAPPUDRAFT_213302, maker-scaffold2255_size18018-snap-gene-0.6 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein DAPPUDRAFT_213302 vs. L. salmonis genes Match: EMLSAG00000000401 (supercontig:LSalAtl2s:LSalAtl2s1063:86108:87342:-1 gene:EMLSAG00000000401 transcript:EMLSAT00000000401 description:”maker-LSalAtl2s1063-snap-gene-0.46″) HSP 1 Score: 149.443 bits (376), Expect = 4.121e-44Identity = 91/196 (46.43%), Postives = 119/196 (60.71%), Query Frame = 0 Query: 14 MDKITDLQVEPLT–NSRFVKPLRLRFKQDGKVKVWDLIQCHASVAVVIFNQTTQKFVFVRQFRPAVYFSALRRAQGDVEPGTQFKGDEIDPKVGITLELCAGIVD-KSKSLIEIAHEEILEETGYDVPMNLIEEIQTFPVGVGVGGENMTLFCAEVTEAMRKGPGGGLAEEGEMIDVIEMGVEETRTLMRAKSVT 206 MDK+ VEPL +SRFV P R+ ++Q+G…

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IRE combined with toripalimab versus IRE alone for LAPC

Introduction Pancreatic ductal adenocarcinoma (PDAC) is a lethal gastrointestinal disease with increasing morbidity, which also has a growing impact on cancer-specific mortality worldwide.1 Nearly 40% of all PDAC cases are localized to the pancreas and characterized with the involvement of major vascular structures, leading to unresectable disease without metastases detected…

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Selection of DNA Aptamers Recognizing EpCAM-Positive Prostate Cancer b

Introduction Prostate cancer (PCa) is one of the most common genitourinary system malignant tumor in men worldwide. In Asian countries, many patients with PCa are often diagnosed at an advanced stage maybe mostly because of a large population base with relatively backward economic development and imperfect cancer screening system of…

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Ensembl vep singularity

Ensembl vep singularity 0 Hello all, I would like to use variant effect prédictor on an hpc cluster. For that i use singularity with the docker image of vep : singularity pull –name vep.sif But i have a problem to use one plugin because a perl module is missing….

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Genomic features of a carbapenem-resistant K. oxytoca strain

Introduction Antimicrobial resistance is a global issue associated with an increased and often unrestricted antibiotic use in clinical settings, which leads to the dissemination of carbapenem-resistant Enterobacterales (CRE) in healthcare facilities (World Health Organization, 2017).1 CRE constitutes a large group of bacteria with different mechanisms for drug resistance. Among them,…

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Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation

Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation 1 I would like to analyze the functional consequence of the mutation in the protein-coding region of the human genome like in TP53 or EGFR etc. I tried Annovar, VEP, SIFT, polyphen, etc but as far…

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SNP of the SREK1 gene is associated with COPD in Kashi

Introduction Chronic obstructive pulmonary disease (COPD) is a chronic respiratory disorder that progresses slowly and is characterized by an obstructive ventilatory pattern, which is rarely reversible. The main risk factors are active smoking, genetic factors, and air pollution. In particular, COPD has been a major public health problem and will…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

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gnomADc plugin instructions not working for VEP

Hi, I have installed VEP for offline use and I am trying to download the data for the gnomADc plugin. The instructions from VEP are as follows; genomes=”storage.googleapis.com/gnomad-public/release/3.0/coverage/genomes” genome_coverage_tsv=”gnomad.genomes.r3.0.coverage.summary.tsv.bgz” wget “${genomes}/${genome_coverage_tsv}” zcat “${genome_coverage_tsv}” | sed -e ‘1s/^locus/#chromtpos/; s/:/t/’ | bgzip > gnomADc.gz tabix -s 1 -b 2 -e 2 gnomADc.gz…

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Mutational Analysis of Mitochondrial tRNA Genes

Introduction Diabetes is a very complex disease characterized by the presence of chronic hyperglycemia. Clinically, insulin-dependent type 1 and non-insulin-dependent type 2 are the main types of diabetes. Among them, type 2 diabetes mellitus (T2DM, [MIM125853]) is a common endocrine disorder affecting approximately 10% of adult population.1 In most cases,…

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Ensembl VEP Plugin not working

Ensembl VEP Plugin not working 0 Hi all… I’m using SubsetVCF plugin to extract some fields from my VCF file when using VEP annotator. I’ve noticed that using VCFv4.1, the plugin works fine but not with VCFv4.2. Are there any limitations to the VCF version that impacts the plugin? Does…

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Classifiers for predicting coronary artery disease

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

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High tumor mutation burden and DNA repair gene mutations

Introduction Anaplastic lymphoma kinase (ALK)‑fusion genes represent a small but important part of oncogenic driver mutations in NSCLC, accounting for approximately 3%‑7% of all cases worldwide.1,2 Small molecule tyrosine kinase inhibitors (TKIs) are the standard therapy for ALK-rearranged NSCLC. Crizotinib, a first-generation TKI, is the most widely used targeted drug…

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Genomic and phenotypic characteristics for Vibrio vulnificus

Background Fisheries and aquaculture are becoming increasingly intensive to meet recent human consumption, resulting in proliferation of marine pathogens and food security concerns.1,2 Vibrio species, as one of the most dangerous foodborne pathogens, cause vibriosis in human around the world.3 It has been reported that vibriosis resulted in 80,000 illnesses…

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Annotate Structural variants with population specific allele frequency values

Annotate Structural variants with population specific allele frequency values 0 Hi, Has anyone tried filtering structural variants based on pupulation specific allele frequency (AF) values (for example gnomAD-SV or phase 3 1000 genome SV)? I have a set of SVs that I detected using a multipronged approach. For prioritising variants,…

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Searching expression for one particular gene in Seurat object issue (Seurat, R)

Searching expression for one particular gene in Seurat object issue (Seurat, R) 0 I don’t know if it’s normal but when I filter my seurat object by a particular gene expression, I have the following results: My gene expression quantiles look like this: `0% 25% 50% 75% 100% : 0.0…

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P. aeruginosa isolated from patients with aural infections

Introduction Aural infections are one of the most common diseases of the head and neck and are predominantly caused by bacterial infections of the ear canal. Several studies from different countries have reported that Pseudomonas aeruginosa is the most common pathogen isolated from ear canal secretions, followed by Staphylococcus aureus.1…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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Gene mutation analysis in papillary thyroid carcinoma

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

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Modification of endoglin-targeting nanoliposomes | IJN

Introduction Today, malignant tumors (cancer) still severely imperil human health and cause millions of global mortality rates.1,2 Deep-seated solid tumors are challenging to cure by most therapeutic tools, mainly blamed on the complex tumor microenvironment (TME).3,4 Adoptive cell therapy (ACT), as one of the effective immunotherapeutic means for cancer treatment,…

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Kaggle Competition Report: SETI Breakthrough Listen

On August 18, the Kaggle SETI competition that I was participating in came to an end. This competition was hosted by Berkeley SETI Research Center, and participants competed on how accurately they can identify anomalous signals from the tremendous amount of data recorded by the Green Bank Telescope. Since we…

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Antibiotic Resistance Genes | IDR

Witawat Tunyong,1 Weewan Arsheewa,2 Sirijan Santajit,3,4 Thida Kong-ngoen,1 Pornpan Pumirat,1 Nitat Sookrung,5,6 Wanpen Chaicumpa,6 Nitaya Indrawattana1 1Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand; 2Department of Microbiology, Phrapokklao Hospital, Chanthaburi, 22000, Thailand; 3School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, 80161, Thailand;…

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Emergence of the Coexistence of mcr-1, blaNDM-5, and blaCTX-M-55 in Kl

Introduction Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen and the leading cause of healthcare-associated infections.1 Multidrug-resistant (MDR) K. pneumoniae isolates are rapidly spreading, thus limiting the choice of antimicrobial agents for empiric treatment of infections caused by these microorganisms; hence, this is a public health challenge.2 Polymyxins are last-resort…

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Nuclear protein in testis carcinoma

Introduction Nuclear protein in testis (NUT) carcinoma (NC) is defined by the rearrangement of the chromosomal region 15q14 harboring the NUTM1 gene. As a clinically aggressive neoplasm with poor differentiation, NC was previously believed to occur primarily in children and young adolescents. However, with an increasing number of reports, middle-aged…

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Bioinformatics Analyst II in Danville, PA for Geisinger

Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research. Performs and supervises complex data extraction, transformation, visualization, and summarization to support Research…

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Infective endocarditis caused by ESBL-EC

Tsuneaki Kenzaka,1,2 Yuto Shinkura,1 Shizuo Kayama,3– 5 Liansheng Yu,3– 5 Sayoko Kawakami,3 Motoyuki Sugai,3– 5 Satoru Kawasaki1 1Department of Internal Medicine, Hyogo Prefectural Tamba Medical Center, Tanba, Japan; 2Division of Community Medicine and Career Development, Kobe University Graduate School of Medicine, Kobe, Japan; 3Antimicrobial Resistance Research Center, National Institute of…

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Vcf file sorting

Vcf file sorting 1 I got vcf file from my instructor. It is VEP annoted with over 50 options separated by ||. I noticed that the vcf is not arrange to appropriate columns so I decided to sort it. I used this code to sort my vcf file according position:…

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VEP plugin uses

VEP plugin uses 0 It is a small question, I downloaded all plugins and wrote in the input script to get plugin experimental functionalities (I am using merged cache Ref_Seq & Ensembl both). # make a file with a single variant using bash echo “17 43071077 43071077 T/C + variant_1″…

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cannot write to FASTA lockfile

Ensembl VEP Docker: cannot write to FASTA lockfile 0 Hello, I am trying to use the Ensembl VEP tool to annotate a database after liftover. For ease of use (or so I thought) I followed all the necessary steps decribed in the official documentation. I want to use local cache…

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Prevalence and Molecular Characteristics Based on Whole Genome Sequenc

Introduction Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the top 10 causes of death worldwide and the leading cause of death from a single infectious agent (ranking above HIV/AIDS).1 In 2020, World Health Organization (WHO) reported that 7.1 million people with tuberculosis were newly diagnosed and notified in 2019,…

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Helicobacter pylori in Pakistan | IDR

Introduction Helicobacter pylori, an infectious agent of human chronic active gastritis and also associated with other gastric ailments such as peptic ulcer, gastric cancer, and mucosa-associated lymphoid tissue lymphoma.1 Clarithromycin is considered the best option among other antibiotics for the management of this bacterial infection.2 However, increasing resistance against this…

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Integrated bioinformatics analysis to identify abnormal CC

Introduction In recent years, the morbidity and mortality of colon cancer have increased rapidly, both being ranked fourth worldwide. Although surgery-based comprehensive treatments improve the prognosis of colon cancer, because of the lack of available means for early diagnosis, the mortality level remains high for patients with advanced-stage cancer. The…

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Gmod error prop

Gmod error prop 24-08-2021 For PC on the PC, a GameFAQs message board topic titled “Why do I get Error messages and purple’ed out maps in Prop Hunt Garry’s Mod?”. Jun 12, @ am. Error Textures,…

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Plasmid-Encoded VIM-2-pProducing Pseudomonas stutzeri | IDR

Introduction Pseudomonas stutzeri is an aerobic, nonfermenting, active, Gram-negative oxidase-positive bacterium with unique colony morphology.1,2 Burri and Stutzer first described it in 1985,3 and the specific metabolic properties, such as denitrification, degradation of aromatic compounds, and nitrogen fixation, distinguish it from other pseudomonads species.2,4 Historically, P. stutzeri was not commonly…

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Interpreting dbNSFP prediction scores

Interpreting dbNSFP prediction scores 1 How should I interpret for example, SIFT score: SIFT_pred = T;T;T;T;D;T SIFT_score = 0.138;0.138;0.138;0.138;0.042;0.157 From dbNSFP documentation, I understand the meaning of D and T D: Deleterious (sift<=0.05); T: tolerated (sift>0.05) My question is: Why there are multiple values of both pred and score in…

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VEP output is only protein_coding

VEP output is only protein_coding 1 Hello, I am supposed to extract both protein coding and synonymous variants from VCFs that were given to me. Only variant consequence i find here is “Protein_coding”, but no strings as “synonymous” are present there. Is that some error with VEP? Thank you! VEP…

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GROMACS: src/gromacs/ewald/pme_pp.h | Fossies

GROMACS: src/gromacs/ewald/pme_pp.h | Fossies “Fossies” – the Fresh Open Source Software Archive Member “gromacs-2021.3/src/gromacs/ewald/pme_pp.h” (18 Aug 2021, 5141 Bytes) of package /linux/privat/gromacs-2021.3.tar.gz: As a special service “Fossies” has tried to format the requested source page into HTML format using (guessed) C and C++ source code syntax highlighting (style: standard) with…

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Bio-DB-HTS installation and ensembl-vep

Bio-DB-HTS installation and ensembl-vep 0 I want to use ensembl-vep with custom annotation. In order to use gff file I need to have library Bio-DB-HTS installed. I downloaded Bio-DB-HTS and used Build.PL with no errors. When I try to install ensembl-vep it still gives an error asking for Bio-DB-HTS library….

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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install ensembl-vep

install ensembl-vep 0 Hello, I want to install ensembl-vep in my Ubuntu 18.04.2. I have already installed LWP::Simple. What can I do in the next step? Thanks in advance for great help! Best, Yue Inspiron-3670:~$ perl -MCPAN -e’install “LWP::Simple”‘ Reading ‘/home/jing/.cpan/Metadata’ Database was generated on Sat, 07 Aug 2021 06:55:53…

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install ensembl-vep

install ensembl-vep 0 Hello, I want to install ensembl-vep in my Ubuntu 18.04.2. I have already installed LWP::Simple. What can I do in the next step? Thanks in advance for great help! Best, Yue Inspiron-3670:~$ perl -MCPAN -e’install “LWP::Simple”‘ Reading ‘/home/jing/.cpan/Metadata’ Database was generated on Sat, 07 Aug 2021 06:55:53…

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