Categories
Tag: ONT
Full 16S and 23S rRNA gene-based,strain-level resolution of the microbiota of a mock bacterial microbiome using ONT nanopore sequencing
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No genes mapped in clusterprofiler gseGO
Hello! I’m having issues generating an adequate geneList for running gseGO in clusterProfiler, using keytype = “GO” Similar issues have been described here: No gene mapped gseGO code is: gse <- gseGO(geneList = gene_List, ont = “ALL”, #ont one of “BP”, “MF”, “CC” or “ALL” OrgDb = OrgDb, minGSSize =…
No gene can be mapped
Hi When I do my data’s Gene Set Enrichment Analysis with ClusterProfiler using codes of Mohammed Khalfan from website, when I run the following code and got the error message. gse <- gseGO(geneList=gene_list, ont = “ALL”, keyType = “ENSEMBL”, nPerm = 10000, minGSSize = 3, maxGSSize = 800, pvalueCutoff =…
Validation of Oxford nanopore sequencing for improved New World Leishmania species identification via analysis of 70-kDA heat shock protein | Parasites & Vectors
Akhoundi M, Downing T, Votypka J, Kuhls K, Lukes J, Cannet A, et al. Leishmania infections: molecular targets and diagnosis. Mol Aspects Med. 2017;57:1–29. Article PubMed Google Scholar Akhoundi M, Kuhls K, Cannet A, Votypka J, Marty P, Delaunay P, et al. A historical overview of the classification, evolution, and…
Single-cell RNA-seq workflow
In this tutorial we walk through a typical single-cell RNA-seq analysis using Bioconductor packages. We will try to cover data from different protocols, but some of the EDA/QC steps will be focused on the 10X Genomics Chromium protocol. We start from the output of the Cell Ranger preprocessing software. This…
Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma
Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…
Study uncovers vast genomic diversity in Aboriginal Australian communities
In a recent study published in the journal Nature, researchers investigated the previously underrepresented genomic diversity of four Aboriginal Australian communities. They used population-scale whole-genome (WGS) long-read sequencing. Study findings revealed unique alleles comprised of insertion-deletion variants, variable copy number regions, and structural variants, 62% of which are novel to…
The landscape of genomic structural variation in Indigenous Australians
Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…
Benchmarking DNA isolation methods for marine metagenomics
Scheme of the study The overall pipeline of our study is presented in Fig. 1 and is described in detail in the methods section. We processed three types of samples: fresh water, sea sediment, and digestive system of a marine invertebrate M. gigas (“gut flora”). These samples were treated in triplicates…
Characterizing viral species in mosquitoes (Culicidae) in the Colombian Orinoco: insights from a preliminary metagenomic study
Kraemer, M. U. et al. The global distribution of the arbovirus vectors Aedes aegypti and Ae. albopictus. Elife 4, e08347. doi.org/10.7554/eLife.08347 (2015). Article PubMed PubMed Central Google Scholar Bhatt, S. et al. The global distribution and burden of dengue. Nature 496, 504–507. doi.org/10.1038/nature12060 (2013). Article ADS CAS PubMed PubMed Central …
London researcher’s AI-enabled test for rare diseases gets $7.5M grant
Article content Artificial Intelligence-led technology developed by a London researcher to help diagnose rare genetic diseases that would otherwise take years to pinpoint may soon be available at labs worldwide after a $7.55-million grant. The work done at London Health Sciences Centre and its research arm, Lawson Health Research Institute,…
Long PCRSeq – Microsynth – CH
Explore expanded possibilities with Microsynth’s Long PCRSeq, leveraging the cutting-edge long-read sequencing technology from Oxford Nanopore Technologies (ONT) to sequence clonal linear DNA ranging from 600 bp to 50 kb in length. Conveniently accessible for samples in tubes and 96-well plates, this service builds upon the capabilities of…
Kinnex launch promises to revolutionize RNA research
RNA sequencing (RNA-seq) has become an indispensable tool for analyzing transcriptomes across all domains of life that can reveal insights about biology and disease. While the genome remains relatively constant for most species over brief time scales, the transcriptome –the sum total of expressed messenger RNA (mRNA) transcripts – varies…
vcfdist: accurately benchmarking phased small variant calls in human genomes
The affine gap design space for selecting variant representations As demonstrated in Fig. 1, the main issue with a difference-based format such as VCF is that often there are multiple reasonable sets of variant calls that can be used to represent the same final sequence relative to a reference FASTA. Since…
Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation
Sample collection A total of nine species of marine fish were collected across three different sampling days (September 7th, 9th, and 12th 2022) under IACUC Animal Use Protocol S12219 (Supplementary Data 1). Six species were collected using a speargun donated by a local fisher. Fish were transported back to shore, euthanized,…
Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
William T. Harvey1, Peter Ebert2,3,4, Jana Ebler2,4, Peter A. Audano5, Katherine M. Munson1, Kendra Hoekzema1, David Porubsky1, Christine R. Beck5,6, Tobias Marschall2,4, Kiran Garimella7 and Evan E. Eichler1,8 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195-5065, USA; 2Institute for Medical Biometry and Bioinformatics, Medical Faculty,…
Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet’s whelk [PeerJ]
Introduction Rapidly advancing next generation sequencing technologies such as whole genome sequencing, genotyping-in-thousands by sequencing (GT-seq), and restriction-site-associated DNA sequencing (RAD-seq), are becoming more available and affordable for non-model organisms (Park & Kim, 2016; Ellegren, 2014; Van Wyngaarden et al., 2017; Bootsma et al., 2020). However, applying these technologies to…
Pipeline for species-resolved full-length16S rRNA amplicon nanopore sequencing analysis of low-complexity bacterial microbiota
Abstract 16S rRNA amplicon sequencing is a fundamental tool for characterizing prokaryotic microbial communities. While short-read 16S rRNA sequencing is a proven standard for examining complex microbiomes, it cannot achieve taxonomic classification beyond genus level. Third-generation sequencing technologies, particularly nanopore sequencing, have allowed for full-length 16S rRNA gene sequencing enabling…
Fetching subsets with slow5curl and samtools
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Overview – Microsynth – CH
Next Generation Sequencing (NGS) is emerging as an exceptionally powerful tool for rapidly unraveling the intricacies of genetic information contained within DNA, RNA or PCR amplicons. Leveraging our deep expertise across multiple NGS platforms, with a particular focus on Illumina and ONT sequencing, Microsynth is proud to position itself as…
KCouper/Liverpool K-means RNAseq Analysis November 2020
R3 VAR14 vs RBC no TNF k-means q0.05 1. Genelist Selection groupsName<-“R3_VAR14_kmeans_q0.05” countsTable<-read.delim(“RNAseq2019July_5.txt”, header = TRUE, sep = “\t”,check.names=FALSE,row.names=1) head(countsTable) AllGeneNames<-countsTable$Gene_Symbol #head(AllGeneNames) tempA<-countsTable topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_0h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_0h))####find indexes listA<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_2h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_2h))####find indexes listB<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_6h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_6h))####find indexes listC<-tempA[ topDEgenes, ]$Gene_Symbol topDEgenes <- which(tempA$padj_R3noTNF_var14_vs_RBC_20h<0.05&!is.na(tempA$padj_R3noTNF_var14_vs_RBC_20h))####find indexes listD<-tempA[ topDEgenes,…
Unleashing the power of soft-decision decodin
image: DNA digital storage (DDS) involves encoding information into nucleotide sequences, synthesizing DNA molecules, and storing them accordingly. Solid-phase synthesis using phosphoramidite-based chemical synthesis can be performed on a column or array solid support, enabling low-throughput or high-throughput synthesis. The synthesized DNA material can be stored in biological cells (in…
Tricorder Tech: UCSC Astrobiologist David Deamer And Mark Akeson Honored For Invention Of Nanopore Sequencing
UCSC’s David Deamer and Mark Akeson won the Golden Goose award for the invention of nanopore sequencing, a transformational technology for reading DNA and RNA. Here, Deamer holds the MinION, a portable device for nanopore sequencing. (photo by Nick Gonzales) [In September 2023] two UC Santa Cruz researchers were honored…
Unleashing the power of soft-decision decoding in DNA digital storage
DNA digital storage (DDS) involves encoding information into nucleotide sequences, synthesizing DNA molecules, and storing them accordingly. Solid-phase synthesis using phosphoramidite-based chemical synthesis can be performed on a column or array solid support, enabling low-throughput or high-throughput synthesis. The synthesized DNA material can be stored in biological cells (in vivo)…
How to deeply sequence long inserts
How to deeply sequence long inserts 1 I have a DNA library encoding scFv antibody genes that consist of VH gene (~380 bp) + linker peptide (54 bp) + VL gene (~380 bp), and the library contains about 1M unique antibodies. We’ve performed some iterative selections on the library such…
Plants | Free Full-Text | The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms
The PacBio RS II sequencer has been effectively utilized to generate a 1.27 Gb genome assembly of Dendrobium officinale [70]. By utilizing advanced sequencing technologies such as Illumina HiSeq, Nanopore, PacBio, and Hi-C, the results have revealed remarkable N50 values of 44 Mb and 65.35 Mb for Gardenia jasminoides and…
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data? 0 I have some cDNA data comparing various mutants to a control sample (each with 3+ replicates) that were obtained using a modified version of the direct cDNA sequencing kit (SQK-DCS109) from ONT. Due to the modified protocol,…
The Biostar Herald for Monday, November 27, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
This commonly prescribed cancer drug was supposed to help save his life, instead it killed him
When Dr Anil Kapoor was diagnosed with stage four colon cancer in January his prognosis was positive, and his family were hopeful that treatment would buy him several more years. But weeks later, the 58-year-old Burlington, Ont., resident was dead — killed not by the cancer, doctors say, but by…
Is It Finally Time To Dump Illumina Stock?
Vive la révolution! It’s not just desperate peasants who embrace radical change of the status quo. Innovations by technology companies are often hailed as revolutionary, disrupting the way we live and work. It’s worth remembering that many revolutionaries later became brutal dictators who ruled over their subjects with an iron…
Technical Applications Scientist – Bioinformatics job with Oxford Nanopore Technologies
Oxford Nanopore Technologies is headquartered at the Oxford Science Park outside Oxford, UK, with satellite offices and a commercial presence in many global locations across the US, APAC and Europe. Oxford Nanopore employs from multiple subject areas including nanopore science, molecular biology and applications, informatics, engineering, electronics, manufacturing and commercialisation….
Is there a good software to generate test genomics data?
Is there a good software to generate test genomics data? 0 For example if I input a reference genome FASTA can I get simulated FASTQ files for ONT sequencing or PacBio sequencing runs that could have produced that data? I’m trying to migrate over from Snakemake to Nextflow but from…
For people doing high molecular weight DNA sequencing library prep, do you see a steep drop off in the fragment sizes before and after the library prep?
For people doing high molecular weight DNA sequencing library prep, do you see a steep drop off in the fragment sizes before and after the library prep? 0 Specifically, I’m wondering does anyone have trouble with magnetic bead clean up on high molecular weight DNA? I extracted some DNA using…
Exome and genome sequencing to unravel the precise breakpoints of partial trisomy 6q and partial Monosomy 2q | BMC Pediatrics
Here, we report a proband with characteristic features of the clinical syndrome, including downward-slanting palpebral fissures; delayed development of bilateral optic nerve hypoplasia; facial deformity with a small mouth, thin lips, micrognathia, and blepharophimosis; short neck; abnormal deciduous teeth; and malformations of the thorax and short ribs. The proband showed…
The Biostar Herald for Monday, November 20, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…
2024 Co-Op, Bioinformatics job with Moderna, Inc.
The Roles: Exciting opportunities to work with Ph.D.-level computational biologists advancing Modernas mRNA therapeutics platform. This application covers three roles. Candidates with interest and skills fitting one or more of these are encouraged to apply. Our co-op program goes from: January 16th to June 14th 2024. All applicants must be…
Evan Eichler, Long Read Sequencing of Complex Genomes | by Axial | Nov, 2023
Axial: linktr.ee/axialxyz Axial partners with great founders and inventors. We invest in early-stage life sciences companies such as Appia Bio, Seranova Bio, Delix Therapeutics, Simcha Therapeutics, among others often when they are no more than an idea. We are fanatical about helping the rare inventor who is compelled to build…
Illumina versus Oxford Nanopore Technologies BUSCO Scores
Illumina versus Oxford Nanopore Technologies BUSCO Scores 1 Hello everyone, I was wondering if anyone has experience using Illumina and Oxford Nanopore Technologies to do a hybrid assembly of genomes? I have illumina and Oxford Nanopore reads and the BUSCO scores are vastly different to each other despite the sequencing…
Oxford Nanopore and Day Zero Diagnostics Partner to Develop a New Class of Bloodstream Infection Diagnostics
OXFORD, England and BOSTON, Nov. 14, 2023 /PRNewswire/ — Oxford Nanopore, the company delivering a new generation of nanopore-based molecular sensing technology, and Day Zero Diagnostics (DZD), an infectious disease diagnostics company harnessing the power of whole-genome sequencing and AI to combat the rise of antibiotic-resistant infections, today announced a collaboration…
Ubuntu Manpage: Bio::Ontology::DocumentRegistry – Keep track of where to find ontologies. Allows lookups
Provided by: libbio-perl-perl_1.7.7-1_all NAME Bio::Ontology::DocumentRegistry – Keep track of where to find ontologies. Allows lookups by name. SYNOPSIS my $registry = Bio::Ontology::DocumentRegistry->get_instance(); my($ont,$def,$fmt) = $registry->documents(‘Sequence Ontology’); my $io = Bio::OntologyIO->new(-url => $ont, -defs_url => $def, -format => $fmt); my $so = $io->next_ontology(); #… DESCRIPTION Do not use this directly, use…
Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance
Sample collection and spiking Chicken fecal samples were collected and processed as follows: one spoonful of fecal material (≈ 1 g) was collected and stored in a DNA/RNA Shield™ Fecal Collection Tube R1101 containing 9 ml of DNA/RNA-shield (Zymo Research, Irvine, CA, USA), according to the manufacturer’s instructions. The sample was mixed…
Real-time analysis of the cancer genome and fragmentome from plasma and urine cell-free DNA using nanopore sequencing
doi: 10.15252/emmm.202217282. Online ahead of print. Ymke van der Pol # 1 2 , Normastuti Adhini Tantyo # 1 2 , Nils Evander 1 2 , Anouk E Hentschel 1 3 , Birgit Mm Wever 1 2 , Jip Ramaker 1 2 , Sanne Bootsma 4 5 6 , Marieke F…
NGS Updates from ASHG: What’s New in Sequencing?
As expected, the NGS companies were sharing their news, out in full force, at the annual American Society for Human Genetics (ASHG) meeting last week in Washington, DC. Whether the updates came from the expo booths showcasing instruments, or users sharing data in the lecture halls, each company had progress…
Capturing human genomic diversity – PacBio
A new Arab pangenome reference has been constructed from 43 individuals enabling the study of variants and sequences of significance to the Arab population. In a newly released preprint entitled A draft Arab pangenome reference, researchers from UAE and several other countries developed both the nuclear and mitochondrial pangenome constructs…
5 Best Genome Sequencing Companies
The Genomic And Multi-omic Revolution The first human genome decoding started in 1990 and was first achieved in 2003. It also cost a staggering $3B. Fast forward 20 years, and the cost of genome sequencing has fallen to $600/genome. Or a 5,000,000x reduction in cost! And it could fall to…
Need Help Understanding Variant Calling Issues in De Novo Yeast Assembly
Need Help Understanding Variant Calling Issues in De Novo Yeast Assembly 0 We have two groups sample of yeast species, control (1 sample) and treatment (1 sample), whose complete reference genome isn’t available yet to do alignment nor variant calling. The objective of this project is straightforward, simply wanting to…
bash – Racon: empty overlap set!
Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then converted from bam to fastq using samtools, then trimmed using nanofilt from there…
DNA Barcoding: A Molecular Toolkit for Species Identification | by Saitama | Nov, 2023
Photo by SilverV 🧬DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. It is a long, thin molecule that carries our genetic code and is coiled up tightly inside the nucleus of every cell in our body. 🧬DNA barcoding is a molecular technology that…
At ASHG, Fabric Genomics Announces Software Deals with Oxford Nanopore, DNAnexus
It’s been a busy week for Fabric Genomics. During the annual meeting of the American Society for Human Genetics in Washington DC this week, the company announced deals with both Oxford Nanopore Technologies and DNAnexus that are aimed at supporting the use of genomic information in clinical contexts. Fabric’s collaboration…
Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria
Isolation of phyllosphere isolates All bacterial strains were isolated in June 2021 from the flag leaves of four wheat cultivars (Sheriff, Heerup, Rembrandt and Kvium) grown in an experimental field in Høje Taastrup, near Copenhagen, Denmark. Wheat flag leaves were picked, pooled, and either washed or blended prior to dilution…
L’essai clinique de Pulsecare Medical sur la technologie nsPFA donne des rsultats satisfaisants de suivi court terme
Class dans : SantSujet : Essais cliniques / Dcouvertes mdicales SHENZHEN (Chine), 31 octobre 2023 /CNW/ – PulsecareMedical, une entreprise innovante de technologie thrapeutique mini-invasive et non invasive, a annonc aujourd’hui que son systme d’ablation en champ puls nanoseconde (nsPFA, nanosecond pulsed field ablation) pour l’lectrophysiologie cardiaque, le premier systme…
Coca Cola, Oxford Nanopore, BP
Three things you need to know in the financial markets today from investment writer, Tony Cross. #1. Coca Cola sees strong revenue growth seen against small volume uptick Coca Cola HBC [LON:CCH] has a Q3 trading update out today, noting another strong trading period. Revenues are up by 15.3% against…
Beyond ATGC: enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA to unlock xenobiology’s potential
Challenging the rules of Nature with unnatural base pairing xenonucleic acids (XNAs) The 4-letter DNA code Nature utilizes (A, T, G, C) is the backbone of the central dogma and the very blueprint of life itself. Our ability to manipulate this code is also the driver of biotechnological progress; everything…
Filtering qscore on dorado
Filtering qscore on dorado 1 I am looking to re-basecall some ONT long-read data which was originally basecalled using Guppy. Previously, with guppy, min_qscore=9. Would it be a good idea to do similar with dorado using the –min-qscore paramater? Or would it be better to filter further downstream of basecalling…
Errors in Functional Enrichment Analysis with Clusterprofiler
Errors in Functional Enrichment Analysis with Clusterprofiler 0 library(clusterProfiler)library(org.Hs.eg.db) library(tidyverse) library(DOSE) library(ReactomePA) library(enrichplot) library(fgsea) library(data.table) library(ggplot2) keytypes(org.Hs.eg.db) res = read.csv(“coex.Csv”) head(res) original_gene_list = res$correlation names(original_gene_list) <- res$gene gene_list<-na.omit(original_gene_list) gene_list = sort(gene_list, decreasing = TRUE) gse <- gseGO(geneList=gene_list, ont =”ALL”, keyType = “ENSEMBL”, minGSSize = 3, maxGSSize = 800, pvalueCutoff =…
That New Nanopore Protein Sequencing Paper
There’s a new nanopore protein sequencing BioRxiv out! It’s well worth a read. But here are my high level thoughts… They design a bunch of synthetic proteins with a bit on the end which the ClpX unfoldase can attach to. This allows them to use ClpX to ratchet the protein…
How to split a folder full of pod5 by phred score?
How to split a folder full of pod5 by phred score? 0 Hi, I’m working on ONT data as pod5 files. Usually, the sequencing device divides the pod5 files in two output folders pod5_pass and pod5_fail. However, this time something failed on that step so I was left with all…
Apply to install Guppy
Apply to install Guppy 0 Hi dear community I really need a GPU version of Guppy(>=3.6.1 version), but I’m not eligible to download Guppy. Could someone who has the ability to download this tool please send a copy to my email?(rogierzhang@126.com) Thank you very much. community.nanoporetech.com/downloads Guppy files fast5 ONT…
Does Guppy have no –fast_out parameters?
Does Guppy have no –fast_out parameters? 0 Dear whom it may concern: I want to obtain the 6mA methylation modification of the genome through the fast5 file of ONT sequencing. The first thing I needed to fix was that the fast5 file from the sequencing company doesn’t have the events…
Whole Plasmid Sequencing Details
Sample Preparation Sample type Size Category Length Concentration Min volume Price per sample Plasmid Regular 2.5 – 25 kb 30 ng/uL ≥10 uL $15 Large 25 – 125 kb 50 ng/uL ≥20 uL $30 XL 125 – 300 kb 50 ng/uL ≥40 uL $60 Linear/Amplicon Standard 600 bp – 25…
Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing
Phuangkum, P., Lair, R. C. & Angkawanith, T. Elephant Care Manual for Mahouts and Camp Managers (FAO Regional Office for Asia and the Pacific, 2005). Google Scholar Sukumar, R. The Asian Elephant: Ecology and Management (Cambridge University Press, 1992). Google Scholar Bansiddhi, P., Brown, J. L., Thitaram, C., Punyapornwithaya, V….
ONT methylation data normalization
ONT methylation data normalization 0 I have methylation data from ONT sequencing expressed as percentage of methylation and/or number of reads. I don’t know if I’m supposed to normalize the data and how to handle replicates. Some ideas: I have data in triplicate. I want to normalize the data (quantile…
Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing
Population and clinical samples The province of Alberta has a population of approximately 4.4 million. During July 19 to December 31, 2022 (the period of this study), molecular testing for SARS-CoV-2 was performed for individuals at risk for severe illness who would benefit from early treatment with antivirals, healthcare workers,…
Researchers develop nanopore sequencing method for mapping disease biomarkers
A nanopore sequencing method that can map dozens of biomarkers at the same time has the potential to transform testing for heart disease and other conditions, say researchers. Scientists at Imperial College London have revealed the results of a research collaboration with Oxford Nanopore Technologies (ONT) in Nature Nanotechnology. The…
Ultra-fast deep-learned CNS tumour classification during surgery
Data simulation Short nanopore sequencing runs yield sparse and random coverage of the genome. To enable model training, we generate simulated sparse nanopore runs based on microarray data. To this end, N simulated reads are randomly sampled from the read length distribution (D) and assigned a start mapping position in…
Prospects of Whole Genome Sequencing in Animal Breeding
Prospects of Whole Genome Sequencing in Animal Breeding The development of high-throughput sequencing technologies has revolutionized animal genetics and genomics. The widespread use of whole-genome sequencing (WGS) allows detection of a full range of common and rare genetic variants of different types across almost the entire genome which facilitates rare…
Over Representation analysis altered pathways in common between comparisons plot
Hi! I did over representation analysis for the comparison group 1 vs group 2, group 1 vs group3 and group 2 vs group 3. I would like to plot an “upsetplot” style plot that has altered pathways for each subgroup has rows and has rows the comparions (e.g group 1…
Functional analysis of differentially expressed circular RNAs in sheep subcutaneous fat | BMC Genomics
Chikwanha, O. C., P. Vahmani, V. Muchenje, M. E. R. Dugan and C. Mapiye (2018). Nutritional enhancement of sheep meat fatty acid profile for human health and wellbeing. Food research international (Ottawa, Ont.) 104: 25–38. doi.org/10.1016/j.foodres.2017.05.005. Khan R, Raza SHA, Schreurs N, Xiaoyu W, Hongbao W, Ullah I, et al….
HycDemux: a hybrid unsupervised approach for accurate barcoded sample demultiplexing in nanopore sequencing | Genome Biology
We have developed a comprehensive pipeline to extract pseudo-barcode regions from raw sequencing data. All of the extracted data is then utilized for subsequent clustering and demultiplexing. In regard to the extracted pseudo-barcode regions, HycDemux integrates an unsupervised hybrid approach to achieve accurate and efficient clustering, in which the nucleotides-based…
Draft genome sequencing of Tilletia caries inciting common bunt of wheat provides pathogenicity-related genes
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…
Progress and challenges in completing the human gene catalogue
In a recent review published in Nature, a group of authors reviewed the progress and challenges in annotating the human genome, including protein-coding genes, isoforms, and non-coding ribonucleic acids (RNAs), and advocated for a universal annotation standard for clinical use. Study: The status of the human gene catalogue. Image Credit:…
BioBam Launches OmicsBox 3.1: Revolutionizing Omics Data Analysis
VALENCIA, Spain–(BUSINESS WIRE)– BioBam, the leading bioinformatics software company, is pleased to announce OmicsBox 3.1, its latest version packed with innovative features designed to empower researchers, scientists, and bioinformaticians in their pursuit of advanced omics data analysis and interpretation. This press release features multimedia. View the full release here: www.businesswire.com/news/home/20231003214238/en/…
Effect of recombination on genetic diversity of Caenorhabditis elegans
Strong correlation exists between recombination rate and abundance and proportion of indels Whole-genome sequence data of many C. elegans wild isolates now exist. These include Illumina paired-end data of over 600 wild isolates by CeNDR, which also obtained first-generation PacBio long-read data of 14 wild isolates. Second-generation PacBio HiFi data20…
Even Tiny Amounts of DNA on Mars Will Be Detectable
The Search for Life is focused on the search for biosignatures. Planetary life leaves a chemical fingerprint on a planet’s atmosphere, and scientists are trying to work out which chemicals in what combinations and amounts are a surefire indicator of life. Martian methane is one they’re puzzling over right now….
GO ENRICHMENT ANALYSIS- DESEQ
I keep getting this Error message: preparing geneSet collections… –> Expected input gene ID: C9orf78,CNOT9,SPIDR,FAM9B,SDC1,CCDC182 Error in check_gene_id(geneList, geneSets) : –> No gene can be mapped…. Here is my code, i attempting to perform gene set enrichement analysis: GroupA <- results(dds, name = "Cancer_Type_healthy_vs_MESO") original_gene_list <- GroupA$log2FoldChange names(original_gene_list) <- GroupA$X…
Scaling logical density of DNA storage with enzymatically-ligated composite motifs
Composite motifs as building blocks for DNA storage A composite motif is a representation of a position in an oligo sequence that uses a combination of motifs drawn from a fixed motif library to encode data. For example, assuming a library of 32 motifs, and a combination factor of four,…
capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements
Cell culture All cell lines were grown in 6 cm dishes at 37 °C in a 5% CO2 incubator. The K562, MDA-MB-231 and HCT 116 cell lines were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics (pen-strep). NCM460 cells were cultured in RPMI 1640 medium supplemented…
the future of mRNA vaccine analysis and quality assurance?
In a recent study published in Nature Communications, researchers proposed a simplified approach for analyzing messenger ribonucleic acid (mRNA) vaccines using long-read sequencing. Study: mRNA vaccine quality analysis using RNA sequencing. Image Credit: Jo Panuwat D/Shutterstock.com Background Messenger RNA vaccines demonstrated safety and efficacy during the COVID-19 pandemic, but extensive…
Deseq2, enrichGO and ensembl ID
Deseq2, enrichGO and ensembl ID 1 @3cc02754 Last seen 5 hours ago United Kingdom Hi I used code initially in DESEQ2 dds=DESeqDataSet(se,design=~TRAIT) dds=DESeq(dds) res=results(dds) I currently have results from DESEq2 which looks like this: log2 fold change (MLE): TRAIT S vs N Wald test p-value: TRAIT S vs N DataFrame…
r – DEseq2 results, enrichGO and ENSEMBL ID not matching
I am trying to do DEG and then use enrichGO on the results. I used code initially in DESEQ2 dds=DESeqDataSet(se,design=~TRAIT) dds=DESeq(dds) res=results(dds) I currently have results from DESEq2 which looks like this: log2 fold change (MLE): TRAIT S vs N Wald test p-value: TRAIT S vs N DataFrame with 42800…
Elusive syntax error in Snakefile
Elusive syntax error in Snakefile 0 Hi, I’m quite new to snakemake and was trying to write a little workflow to analyze some nanopore data. However, it keeps returning an invalid syntax error caused by this rule rule alignment: input: “{base_out}/2.TRIMMING/{sample}.trimmed_and_clean.fastq.gz” output: “{base_out}/3.ALIGNMENT/{sample}.ngmlr.bam”, “{base_out}/3.ALIGNMENT/{sample}.ngmlr.bai” resources: partition: “EPYC” runtime: 5760 mem_mb:…
DNA sequencing at the picogram level to investigate life on Mars and Earth
All the extractions, dilutions and library preparation for sequencing were carried out inside the clean room environment of ISO (International Organization for Standardization) level 5 (ECSS-Q-ST-70-55C standard)32. An ISO 5 Class clean room is a semi-closed ultra clean environment that utilises High Efficiently Particle Air (HEPA) filtration systems to maintain…
purge_dups removes too much sequence
assembly: purge_dups removes too much sequence 0 I have tried out purge_dups and found results to be puzzling. First, there seems to be a silent bug where contig fasta headers are ignored (symptom – bed files are empty). Solution – use simple contig fasta headers, like sample_contig1 and not sample-complex-name_x1-_contig-1….
Explanation needed for POD5 files- channel ID’s, PromethION run
Explanation needed for POD5 files- channel ID’s, PromethION run 1 Hello! I am new to processing ONT data. I am running a split-read-by-channel command (below), so that I can run dorado duplex basecalling on the reads more efficiently. pod5 view /path/to/pod5s –include “read_id, channel” –output summary.tsv I have, say, 2000…
Pacific Biosciences: Attractive in the Fast-Growing DNA Sequencing Market (NASDAQ:PACB)
Editor’s Note: Seeking Alpha is proud to welcome DZ Research as a new contributor. It’s easy to become a Seeking Alpha contributor and earn money for your best investment ideas. Active contributors also get free access to SA Premium. Click here to learn more “ ebrublue10 My essay The goal…
Pacific Biosciences: Appealing In The Fast-Growing DNA Sequencing Market (NASDAQ:PACB)
Editor’s note: Seeking Alpha is proud to welcome DZ Research as a new contributor. It’s easy to become a Seeking Alpha contributor and earn money for your best investment ideas. Active contributors also get free access to SA Premium. Click here to find out more » ebrublue10 My thesis Goals…
Long read filtering based on reference
Long read filtering based on reference 0 Hi everyone!! I’m diving into the world of long read sequencing. I want to do some quality filtering of my reads using Filtlong (github.com/rrwick/Filtlong). According to the author filtering using a reference is a better way to go in comparison to quality parameter…
Iso-Seq method outperforms other long-read methods in benchmarking consortium study
A benchmarking of long-read RNA sequencing methods and analysis tools The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) consortium, an initiative to systematically evaluate methods for transcript identification and quantification, recently released their final assessment of long-read sequencing technologies and tools in the preprint “Systematic assessment of long-read RNA-seq methods…
Which minimap2 parameters to set while performing mapping to avoid such mismatches
Which minimap2 parameters to set while performing mapping to avoid such mismatches 1 Hi all, Apologies that I don’t have a lot of experience with this stuff, but It’s been a long time since I am struggling with this issue. I am aligning my RNA seq data of a heterologous…
Emergence of ST248Pasteur-ST1068Oxford | IDR
Acinetobacter pittii is a crucial pathogen that mainly causes healthcare-associated infections, including pneumonia, bloodstream infections (BSIs) and urinary tract infections (UTIs).1 Carbapenem-resistant A. pittii (CRAP) poses a huge challenge in clinical settings. CRAP is increasingly recognized as a significant pathogen of hospital-acquired infections in the hospital.2 Carbapenem resistance in A….
Load MF, CC and BP from org.Hs.eg.db
Hi! I would like to load all the pathways related to CC, MF and BP from the org.Hs.eg.db, converting into a dataset that has as columns pathway, gene_symbols. In order that after this I filter the pathways that have genes in common with the metabolism pathways from KEGG. So that…
Assembly of 43 human Y chromosomes reveals extensive complexity and variation
Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article ADS CAS PubMed Google Scholar Porubsky, D. et al. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 185, 1986–2005 (2022). Article …
Microorganisms | Free Full-Text | Genome-Wide and 16S rRNA Sequencing-Based Analysis on the Health Effects of Lacticaseibacillus paracasei XLK401 on Chicks
1. Introduction Since 2006, the European Union has prohibited the use of antibiotics in animal feed to boost growth [1]. This ban has resulted in a significant rise in disease outbreaks in broiler farming [2]. Therefore, there is an urgent need to find effective antibiotic alternatives for use in the…
Moderna hiring 2024 Co-Op, Bioinformatics in Cambridge, Massachusetts, United States
The Roles:Exciting opportunities to work with Ph.D.-level computational biologists advancing Moderna’s mRNA therapeutics platform. This application covers three roles. Candidates with interest and skills fitting one or more of these are encouraged to apply.Our co-op program goes from: January 16th to June 14th 2024. All applicants must be available for…
A tool for rapid, automated characterization of population epigenomics in plants
Creation and sequencing of epigenetically diverse plant populations To induce epigenetic variation, A. thaliana seeds were treated with three different concentrations of zebularine. We will describe these three different zebularine concentration groups, and our water and DMSO controls as “populations” throughout the remainder of this paper. Plants displayed stunted vegetative…
Over Representation Analysis over one specific pathway
Over Representation Analysis over one specific pathway 0 Hi! Let’s say I would like to analyse if a particular pathway is enriched how would I do that given that I have a set of DGE genes resulting from 1500 genes of RNA Seq? I do not want to analise any…
Coverage histogram query
Coverage histogram query 0 Hi, I was just wondering if anyone has seen a genome coverage histogram as the green one and have any explaination for the same? This plot is generated after aligning ONT long reads to the human genome. Regards, Prasun Alignment • 58 views Login before adding…
Protein Sequencing Expands the Omics Club
The most exclusive club in omics has admitted only genomics and transcriptomics, the beneficiaries of single-molecule sequencing technologies that are so powerful they enable highly refined single-cell and spatial analyses. In contrast, proteomics has been underprivileged with respect to sequencing. But proteomics is about to enjoy a change in fortune….
Enricher with Gene Symbols
Enricher with Gene Symbols 0 Hi! I have a list of genes with abs(logfc) >= 0.9 like this: > genes [1] “MDM2” “CDK4” “CCND2” “FLNA” “RBP7” “EDNRB” “EPHA4” “PTPRB” “PPP1R13L” “TPM1” “INSR” [12] “DLC1” “WNT7B” “SFRP1” “IFI16” “ZMAT3” “MEST” “AKT3” “CD36” “SRD5A1” “KIF23” “EPOR” So the list has the gene…
Insider Clive Brown’s Share Purchase Signals Confidence in Oxford Nanopore Technologies’ Future
Oxford Nanopore Technologies Insider Clive Brown Acquires Shares: An Intriguing Move Signals Confidence in Company’s Future Date: August 14, 2023 In an intriguing turn of events on August 11th, 2023, Clive Brown, an insider at Oxford Nanopore Technologies plc (LON:ONT), made a significant purchase of company shares. This unexpected move…