Tag: ENA

Termy February 8, 2024, 10:59am 1 Hi there,i’m finally coming around to update to 23.05 and just want to make sure to not F* up something I want to keep TLS1.3 and thus openSSL. Of course, the image build fails if i just include libustream-openssl.It build successfully if i also…

Animals and samples The study included 10 pigs, 8 pigs were bred at the INRAE experimental farm (doi.org/doi.org/10.15454/1.5572415481185847E12) and 2 pigs come from breeding organizations in accordance with the French and European legislation on animal welfare. The animals belong to the same family, except for one LW animal. Animals were…

My paired end data became single end data after mapping 1 Dear community, Something weird happened to me, my public dataset is obviously paired-end data (stated in ‘metadata’ part of ENA database, and there are two seperate fastq files (R1 & R2) and index file (I1) per sequencing run). After…

  Q&A Report from the workshop: QuestonWha is he bes msa ool?clusal 2 and clusal omega are he sameHow would we ener multple sequences? because here is only one inpu boxCould he legend explaining symbiols (*, -,…) be shown in he resul window?Wha is he max number of sequences one…

Título:  Autor:  Garrigós, Marta; Ylla, Guillem CSIC ORCID; Martínez de la Puente, Josué CSIC ORCID; Figuerola, Jordi CSIC ORCID ; Ruiz-López, María José CSIC ORCID Palabras clave:  TranscriptomesAvian malariaCulexGene expresion Fecha de publicación:  12-dic-2023 Editor:  DIGITAL.CSIC Citación:  Garrigós, Marta; Ylla, Guillem; Martínez de la Puente, Josué; Figuerola, Jordi; Ruiz-López, María…

Abstract Inflammatory bowel disease (IBD) is associated with dysbiotic microbiomes. However, whether microbiomes of family members of IBD patients harbour microbial disease signatures of IBD is unknown. Here, we generate shotgun metagenomic data of an IBD family cohort and treatment-naive IBD cases, which we combine with published IBD metagenomes, to…

4 Fastq files for a single run generated by 10X 0 Hello, I have a question about the 10X generated Fastq files. As I know 10X platforms can generate up to 4 Fastq files as R1, R2, I1 and I2. I need to use Fastq files and align them with…

Abstract While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2–27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal…

Abstract The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe’s only intergovernmental life sciences organisation. This…

Image by Gerd Altmann from Pixabay For downloading data and standardized metadata from GEO (Gene Expression Omnibus) and SRA (Sequence Read Archive), several bioinformatics and command-line tools and scripts are available, primarily hosted on GitHub. ARA: An automated pipeline developed for better sampling of NCBI SRA database records, allowing full…

Product Data Locus ID 2994 Synonyms CD235b; GPB; GYP; GYPA; MNS; PAS-3; SS Vector pGFP-C-shLenti E. coli Selection Chloramphenicol (34 ug/ml) Mammalian Cell Selection Puromycin Format Lentiviral plasmids Kit Components GYPB – Human, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene ID = 2994). 5µg purified plasmid DNA per…

Williamson, C. E., Saros, J. E., Vincent, W. F. & Smol, J. P. Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnology and Oceanography 54, 2273–2282, doi.org/10.4319/lo.2009.54.6_part_2.2273 (2009). Article  ADS  Google Scholar  Cavicchioli, R. et al. 2019. Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews…

How to download FASTQ files from the European Nucleotide Archive (ENA) to use them with FastQC etc.. 2 Hello, I would like to download FASTQ files from the European Nucleotide Archive (ENA) to use them with FastQC, kallisto,etc. In particular, this: www.ebi.ac.uk/ena/browser/view/PRJEB31975 Since it’s a huge amount of data, how…

Hello, How can I extract useful information from RNA Seq data from “BioStudies, Array Express” website? www.ebi.ac.uk/biostudies/arrayexpress/studies I want to create a machine learning model to correctly classify LTBI and active TB patients using this data: www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-7830 The raw data is: www.ebi.ac.uk/ena/browser/view/PRJEB31975 I mean, through R or Python, how can…

The anti-dsDNA test is a blood test used to detect antibodies against double-stranded DNA. Antibodies are molecules produced by the immune system to combat foreign substances and pathogens. In some autoimmune diseases, these antibodies mistakenly attack the body’s cells and components. One specific antibody, Anti-dsDNA, specifically recognizes and binds to…

Located on the southeastern coast of Australia, Melbourne is one of the leading life science hubs in the Asia Pacific region, according to a CBRE report published in 2021. With more and more investors taking an interest in the Melbourne region, this contributes to the country’s market value of $170…

The indirect fluorescent antibody detection of anti-dsDNA uses which of the following as the antigen source? A) Hep 2 cell cultures B) mouse stomach sections C) Crithidia lucilliae kinetoplast D) monkey kidney cellsWhat type of antibodies are indicated by a positive peripheral or rim pattern observed on an ANA test?…

doi: 10.1093/nar/gkad903. Online ahead of print. Affiliations Expand Affiliation 1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA. Item in Clipboard Eric W Sayers et al. Nucleic Acids Res. 2023. Show details Display options Display options Format AbstractPubMedPMID…

Parasite culture, maintenance, synchronization and transfection The DiCre-expressing P. falciparum clone II3 (ref. 10) was maintained in human A+ erythrocytes at 37 °C in Roswell Park Memorial Institute 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM l-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using…

EMBL stands as a leader, exemplifying how to harmoniously integrate AI in research and through its delivery of data services   Ewan Birney, Deputy Director General of EMBL and Director of EMBL-EBI. Photo credit: Jeff Dowling/EMBL-EBI By Ewan Birney, Deputy Director General of EMBL and Director of EMBL’s European…

My NGS bioinformatics analysis starts with an amplicon FASTQ file (only the R1). In my workflow, I finally created a BAM file. Then, I convert this BAM in CRAM for backup apptainer exec –bind “$ref_folder”:”$ref_folder” “$samtools” samtools view \ -C -T $bwarefgenomepath \ -o ART03_FINAL.cram \ ART03_FINAL.bam We will backup…

Best command line tool for downloading sequencing reads 2 Hello there, I am using enaBrowserTools (enaDataGet) for bulk downloading raw reads from ENA in a pipeline of mine. The last few weeks I noticed that I am getting this error message a lot when I use this tool Error with…

Lirafugratinib (RLY-4008) demonstrated clinical activity in multiple subsets of patients with FGFR2-altered solid tumors, including those with FGFR2-altered hormone receptor–positive, HER2-negative breast cancer, according to data from the phase 1/2 ReFocus trial (NCT04526106) presented at the 2023 AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics.1,2 Efficacy with the agent…

Zhang L, Wang F, Wang L, Wang W, Liu B, Liu J, Chen M, He Q, Liao Y, Yu X, et al. Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet. 2012;379:815–22. Article  PubMed  Google Scholar  Collaboration GBDCKD. Global, regional, and national burden of chronic kidney disease, 1990–2017:…

1Indian Agricultural Research Institute (ICAR), India 2Uttarakhand University of Horticulture and Forestry, India The final, formatted version of the article will be published soon. Notify me Receive an email when it is updated You just subscribed to receive the final version of…

PMPrimer software PMPrimer is a Python-based tool for the automated design and evaluation of multiplex PCR primer pairs for specific targets using diverse templates (Fig. 1). To satisfy the need for automation, PMPrimer can directly extract taxonomic information at three levels of classification (genus, species, and subspecies) from input data in…

Learn about the tools, processes, and analysis approaches used by MGnify in the field of genome-resolved metagenomics. This course will cover the use of publicly available resources to manage, share, analyse, and interpret metagenomics data, focussing primarily on the assembly-based approaches used in MGnify analysis. The delivered content will involve…

Source: Youtube.com The era of big data has revolutionized the way we analyze and interpret complex biological systems. In the field of genomics, Chip-Seq (Chromatin Immunoprecipitation Sequencing) data has become a valuable resource for understanding gene regulation and the functionality of the genome. Chip-Seq data provides insights into the binding…

[RFC PATCH 1/2] MIPS: AR7: remove VLYNQ init – Wolfram Sang From: Wolfram Sang <wsa@kernel.org> To: linux-kernel@vger.kernel.org Cc: Florian Fainelli <f.fainelli@gmail.com>, Greg KH <gregkh@linuxfoundation.org>, Wolfram Sang <wsa+renesas@sang-engineering.com>, Thomas Bogendoerfer <tsbogend@alpha.franken.de>, linux-mips@vger.kernel.org Subject: [RFC PATCH 1/2] MIPS: AR7: remove VLYNQ init Date: Sat, 16 Sep 2023 11:11:23 +0200 [thread overview] Message-ID:…

Introduction Infective endocarditis (IE), as a disease first recognized in 1885, is defined by infection of a native or prosthetic heart valve, the endocardial surface, or an indwelling cardiac device.1–3 Despite advances in diagnostic capabilities and treatment options, IE remains a rare condition but with high associated mortality. And epidemiological…

I am validating a flatfile of an annotated chloroplast genome scaffold. It includes /organism=”Cannabis sativa” and /organelle=”plastid:chloroplast”. This means the CDS should be translated according to the bacterial translation table and I therefore included the /transl_table=11 qualifier in my CDS annotations. See head of of the flatfile below (some info…

Ensembl Oryza sativa indica genome was submitted by Beijing Genomics Institute: www.ebi.ac.uk/ena/browser/view/GCA_000004655.2 If the MSU genome came from the same submission then they should be identical. There are a total of 25 indica genomes available in NCBI www.ncbi.nlm.nih.gov/datasets/genome/?taxon=39946 but out of the lot one referred to above seems to be…

image: How refget works view more  Credit: Stephanie Li / GA4GH   A widely-used tool that finds the exact references needed to pinpoint differences in our DNA just got a refresh. On 17 July, the Standards Steering Committee of the Global Alliance for Genomics and Health (GA4GH) voted to release refget v2.0….

How refget works. Credit: Stephanie Li / GA4GH A widely-used tool that finds the exact references needed to pinpoint differences in our DNA just got a refresh. On 17 July, the Standards Steering Committee of the Global Alliance for Genomics and Health (GA4GH) voted to release refget v2.0. With better…

Tool:sra-explorer : find SRA and FastQ download URLs in a couple of clicks 0 Hi all, As a fun little side project I’ve made a web tool to find runs on the NCBI Sequence Read Archive (SRA) and fetch the download URLs for these. You can do all of this…

CHESHAM, England, July 7, 2023 — Resolve Optics installed and commissioned a new vibration test center adding to the suite of in-house lens-testing equipment the company is able to offer. Lenses used in harsh industrial inspection and military and space applications are often exposed to vibrations, shocks, temperature changes, radiation,…

EMBL’s European Bioinformatics Institute (EMBL-EBI) has launched the Pathogens Portal—an online platform that enables researchers, clinicians, and policymakers to access the most comprehensive collection of biomolecular data about pathogens. The portal features data spanning over 200,000 pathogen species and strains and is set to become a key tool for infection…

Credit: dottedyeti/stock.adobe.com Summary EMBL-EBI’s new Pathogens Portal enables sharing and analysis of pathogen data from across the world The Portal makes it easier for scientists, healthcare, and public health professionals to collaborate, enhancing pathogen surveillance worldwide Being able to share pathogen data across borders is crucial, especially during public health…

fastq.gz how to split. 1 Good morning everyone, I am download the fastq files for study GSE132802 through www.ebi.ac.uk/ena/browser/view/PRJNA549083. This is paired fastq file, but I only got one fastq file. I am considering split it. But I am not sure what is the best way to do it. I…

Are you passionate about using bioinformatics to unravel the mysteries of biology and make a positive impact on human health? We have an incredible contract opportunity for a talented Bioinformatics Analyst to join our dynamic team. As a Bioinformatics Analyst, you will have the chance to design and implement cutting-edge…

Talentify helps candidates around the world to discover and stay focused on the jobs they want until they can complete a full application in the hiring company career page/ATS. Seeking a Bioinformatics Analyst 100% Remote Description Support of computational research priorities associated with oncology discovery programs. This variably entails querying…

How to deal with SRA file without .SRA 0 Good afternoon, I have encountered a problem with an SRA file and I hope you can help me. I downloaded the SRA file from this website: www.ebi.ac.uk/ena/browser/view/PRJNA834732. I obtained the SRA file without the .SRA extension. I used fast-dump to extract…

Title: Bioinformatics Analyst III Duration: 12 Months Location/Site: 100% Remote Pay Rate: $51/hr. – $56/hr. on w2 Job Description Services Overview: Services include support of computational research priorities associated with oncology discovery programs. This variably entails querying public cancer genomics resources for mutation/expression distributions, assessing normal expression, interpreting germline associations…

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We are looking to hire a capable Bioinformatics Analyst to join our passionate team at Synectics Inc in North Chicago, IL.Growing your career as a Full Time Bioinformatics Analyst is a terrific opportunity to develop relevant skills.If you are strong in planning, problem-solving and have the right experience for the…

Remote role Title – Bioinformatics Analyst We have an exciting contract opportunity for a Bioinformatics Analyst with extensive experience in designing and implementing bioinformatics methods as well as analysis and interpretation of various types of omics data to solve biological and clinical problems. The candidate should be familiar with developing…

Remote role Title – Bioinformatics Analyst We have an exciting contract opportunity for a Bioinformatics Analyst with extensive experience in designing and implementing bioinformatics methods as well as analysis and interpretation of various types of omics data to solve biological and clinical problems. The candidate should be familiar with developing…

Title – Bioinformatics AnalystTypically between 9 AM-5 PM Central Time.Remote We have an exciting contract opportunity for a Bioinformatics Analyst with extensive experience in designing and implementing bioinformatics methods as well as analysis and interpretation of various types of omics data to solve biological and clinical problems. The candidate should…

Carlson, J. L., Erickson, J. M., Lloyd, B. B. & Slavin, J. L. Health effects and sources of prebiotic dietary fiber. Curr. Dev. Nutr. 2, nzy005 (2018). Article  PubMed  PubMed Central  Google Scholar  Deehan, E. C. et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid…

Abstract Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein…

The UKB is approved by the North West Multi-centre Research Ethics Committee (www.ukbiobank.ac.uk/learn-more-about-uk-biobank/about-us/ethics). The current study was conducted under UKB application no. 26041. The data in the UKB were collected after written informed consent was obtained from all participants. The Human Research Committee of the MGB approved the Biobank research…

Nucleotide databases are repositories that store and provide access to nucleotide sequence data. These databases contain a vast collection of DNA and RNA sequences from various organisms, including viruses, bacteria, plants, animals, and humans. Nucleotide databases play a crucial role in genomics, molecular biology, and bioinformatics research by providing a…

2 hours ago Article URL: www.ncbi.nlm.nih.gov/genbank/ Comments URL: news.ycombinator.com/item?id=36038722 Points: 1 # Comments: 0 GenBank OverviewWhat is GenBank?GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which…

This page presents an annotated sample GenBank record (accession number U49845) in its GenBank Flat File format. You can check the corresponding alive record for U49845, and seeexamples of other records the show a range of biological features. SITE SCU49845 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene,…

Figure 1 shows the detailed workflow of the study. Fig. 1 General overview of the study. Briefly, MPXV was isolated from a skin lesion and then was used to infect CV-1 cells. After the designated infection times, total RNA was isolated and sequenced using direct cDNA sequencing protocol on ONT’s MinION platform….

Issue about generating EMBL Flat file for ENA submission 0 Hello all! I am trying to generate an EMBL flat file to submit an annotated assembly to ENA. I am using EMBLmyGFF3 to generate the flat file from the whole genome FASTA file and the GFF3 file. I am getting…

1. Introduction Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella, which affects domestic livestock and a wide range of wild mammals (Ducrotoy et al., 2017). The disease is amongst the most common zoonotic infections globally, with an estimated 500,000 human cases annually (Pappas et al., 2006),…

During the COVID-19 pandemic, one online platform emerged as the main repository for viral genome data. GISAID, an initiative launched in 2008 to improve the global sharing of influenza data, earned the trust of scientists by ensuring that they would be credited for the data they generated. It now hosts…

Bergqvist, C. et al. Neurofibromatosis 1 French national guidelines based on an extensive literature review since 1966. Orphanet J. Rare Dis. 15, 1–23 (2020). Article  Google Scholar  Martin, G. A. et al. The GAP-related domain of the neurofibromatosis type 1 gene product interacts with ras p21. Cell 63, 843–849 (1990)….

Issue With CRAM -> BAM -> FASTQ Conversion 2 Please help! I am trying to obtain fastq files from the GDSC, all we have in the lab is CRAM files. Unfortunately, the reference genome seems to not exist when pulled from an online source. I have attempted to use the…

curl -s “https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33024307/datalinks?format=json” | jq ‘.'{ “version”: “6.8”, “hitCount”: 9, “request”: { “id”: “33024307”, “source”: “MED” }, “dataLinkList”: { “Category”: [ { “Name”: “Nucleotide Sequences”, “CategoryLinkCount”: 5, “Section”: [ { “ObtainedBy”: “tm_accession”, “Tags”: [ “supporting_data” ], “SectionLinkCount”: 5, “Linklist”: { “Link”: [ { “ObtainedBy”: “tm_accession”, “PublicationDate”: “04-11-2022”, “LinkProvider”: { “Name”:…

Creating a reference panel of equus caballus sequences 1 Hi all, I have a quick question regarding the starting of my masters project that I’m trying to understand, I am currently trying to create a reference panel of wgs for the species equus caballus (horse) as part of my research…

The impact of X overdosage on the global transcriptomes of Saudi and ENA KS-iPSCs. A) Venn diagram showing the DEGs shared in the contrast 47,XXY Vs. 46,XY in iPSCs generated from ENA and Saudi KS patients. B) Gene Ontology analysis on common DEGs using the GO enriched for Biological Processes…

I’m attempting to do a strainphlan analysis of Blautia wexlerae, but nothing I’m doing is working. I think the problem might be the reference genomes that I’m using, but I’m using the 2 primary genomes from NCBI. Is there another place to get correctly formatted references? Error Here’s the primary…

We release metagenomic data of seven urban, eutrophic Swedish lakes that have been extensively studied and characterized in terms of biogeochemistry. Here we provide the supplementary tables and the full set of metagenome-assembled genomes of 17 metagenomic samples. – We have 10 metagenomic samples from Lake Mälaren which is the…

Introduction Colorectal cancer (CRC) is a leading cause of cancer-related death1 and its mortality rate is expected to rise worldwide, due to population growth and aging, thus entailing a global public health challenge. CRC mortality is mainly due to therapy resistance and metastasis, which are driven by a small population…

Obtain number of base pairs in a genome 1 HI! It’s going to be a stupid question since I’m not anyhow related to bioinformatics – I’m interested into how can I obtain the number of base pairs in my genome sample. I’m trying to remake the experiment that was made…

Let me show you an example: trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR16093385&display=metadata This data contains two reads, R1 and R2. The read length of R1 and R2 are the same 150bp. However, this experiment is performed following 10x 3’library protocol. In the method section, it described as below: The scRNA-seq libraries were generated using the…

Ensuring open data from landmark biodiversity projects and smaller genome sequencing initiatives are readily-available to the global scientific community Genomic data for biodiversity research is produced and shared worldwide. Credit: Karen Arnott/EMBL-EBI As major biodiversity projects increasingly use genomic sequencing to catalogue and understand species, EMBL-EBI is ensuring that the…

Error while converting GFF file to GTF using AGAT 0 Hi I am trying to convert a gff file to gtf file which I want to use for STAR. I tried AGAT(latest version) to convet but it gives me a series of error(mailny tow types) .I have attached the error…

Harmonizing datasets for eQTL and co-regulation analysis We combined 14 eQTL datasets into the ‘MetaBrain’ resource to maximize statistical power to detect eQTLs and create a brain-specific gene co-regulation network (Fig. 2, Supplementary Figs. 1–7 and Supplementary Table 1). Previous to quality control (QC), MetaBrain includes 7,604 RNA-seq samples and…

Hi, I am new to Single cell analysis but have some experience with NGS data output and manipulation. I have a set of .bam that I assume were the product of the cell ranger pipeline from the ENA (project ID PRJEB36998) unfortunately I have no access to any other output…

P. aeruginosa bacterial strains Reference strains Four well-described and genome-available reference strains were used in the present study, ATCC27853 and ATCC15442, obtained from the American Type Culture Collection (ATCC), and PAO1 and PA14, from the collection of Institut Pasteur (Paris, France). Strain ATCC15442 is recommended for disinfectant susceptibility testing44, strain…

Alignment in bioinformatics 1 my project talk about gene expression profile of Mycobacterium tuberculosis on lung , i choose my samples from ENA :www.ebi.ac.uk/ena/browser/view/PRJEB19976 , I download reference genome from NCBI : www.ncbi.nlm.nih.gov/genome/?term=h37rvand , I create an index by myself using HISAT2 and after that i started the process of…

NEW YORK – The Institut Pasteur in Paris has won €2 million ($2.1 million) in EU funding to create a “search engine for DNA sequencing data,” indexing next-generation sequencing data available in the Sequence Read Archive in order to make it searchable and more accessible. The five-year IndexThePlanet project, led…

Tellus Solutions is in partnership with a committed biopharmaceutical company in North Chicago focused on providing innovative therapies. Your technical expertise as a Bioinformatics analyst in the area of using R to do basic data analysis (processing, plotting), RNA-Seq alignment experience will contribute to our client’s innovative therapies which will…

HHS Vulnerability Disclosure, Help This document is an overview of the Entrez databases, with general information on If you are not sure that the “Save” option in your program will do this for you, use “Save As”, In Excel, select “Save As” from the File menu. optimizations to reduce memory…

WALTHAM, Mass. and BOULDER, Colo., Oct. 26, 2022 (GLOBE NEWSWIRE) — Cogent Biosciences, Inc. (Nasdaq: COGT), a biotechnology company focused on developing precision therapies for genetically defined diseases, today announced that it will be presenting two preclinical posters at the EORTC-NCI-AACR (“ENA”) annual meeting to be held October 26-28, 2022. Presentations…

Job description Tellus Solutions is in partnership with a committed biopharmaceutical company in North Chicago focused on providing innovative therapies. Your technical expertise as a Bioinformatics analyst in the area of using R to do basic data analysis (processing, plotting), RNA-Seq alignment experience will contribute to our client’s innovative therapies…

Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…

Provided by: biobambam2_2.0.179+ds-1_amd64 NAME bamfillquery – fill query sequences into BAM files SYNOPSIS bamfillquery [options] <in.bam queries.fasta >out.bam DESCRIPTION bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting data…

Hi, all! I download fastq.gz files of GSE162708 from ENA which only have 2 files of each sample(usually scRNA-seq has 3 files I1 , R1 & R2 ). Then I run fastp as following Then I get QC report , but I can’t understand why Per base sequence content of…

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…

A worldwide consortium of scientists, led by the Earlham Institute and the University of Liverpool, has developed an efficient, inexpensive approach to large-scale bacterial genome sequencing that could equip researchers in low- and middle-income countries (LMICs) with cheap and accessible methods for sequencing large collections of bacterial pathogens—at a cost…

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,…

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…

These datasets reuse the globally comprehensive DNA sequence data that ENA and its partners, the National Centre for Biotechnology Information (NCBI)  and the DNA Data Bank of Japan, maintain in the International Nucleotide Sequence Database Collaboration (INSDC). EMBL-EBI maintains ENA, which supplied the first DNA-derived dataset shared through GBIF in…

Data provision and standards. GEO sequence submission procedures are designed to encourage provision of MINSEQE elements: Thorough descriptions of the biological samples under investigation, and procedures to which they were subjected. Thorough descriptions of the protocols used to generate and process the data. Request updates to accessioned records per the…

The faces of three ancient Egyptians are brought back to life thanks to DNA group of scientists Recreate The faces of three ancient Egyptian men using DNA that is more than 2,000 years old. According to the magazine NEWSWEEKIt is believed that this is the first time that modern techniques…

The faces of three ancient Egyptian men have been brought to life by scientists, using DNA that is more than 2,000 years old. This is thought to be the first time modern techniques have been used on human DNA of this age, with the trio of samples estimated to be…

New Snapshot methods for low-coverage sequencing bring hidden data to life Scientific Poster Image Scientific Poster Image Scientific Poster Image RESTON, Va., Sept. 15, 2021 (GLOBE NEWSWIRE) — At the 32nd International Symposium on Human Identification (ISHI), being held this week in Orlando, Florida, Parabon NanoLabs will unveil for the…

I downloaded fastq files from a repository and tried to run fastqc, how can the average sequence length be only 8 bp? 1 I downloaded sequencing files from 2 patients from here: www.ebi.ac.uk/ena/browser/view/PRJNA588461?show=reads there is one fastq file for the forward (1) and reverse (2) reads. I wanted to look…

project number: PRJNA505380 An example of Run accession: SRR8244780 Issue: Inconsistency between the library layout of Run and data source. As the library layout both in ENA and SRA labeled, Runs in Bioproject PRJNA505380 should be pair-end reads data. But some of them only have a single fastq and without…

Forum:Sequence (annotation) databases in 2021 1 Hi everyone, So I know there are several threads on this topic already (or tangentially related to it). For example: But these threads are really old now. Things have probably changed quite significantly in the mean time. So I would like to start a…