Tag: ONT

Issue Title State Comments Created Date Updated Date Mapping reads against multi references. Any proposition? open 0 2022-06-28 2022-06-30 Inversion between tandem repeats yields misalignment closed 1 2022-06-21 2022-06-30 use minimap2 to extract mitochondrial reads from genome assembly open 0 2022-06-20 2022-06-30 Asking for #301 to be reopened closed 0…

Get reference genome from Kraken2 taxID 0 I have a ~10Gb ONT metagenome from citrus psyllid that I am trying to extract bacterial contigs from to assemble. My current thought for a pipeline is broadly as follows: Tentative ID of each contig with Kraken2, then QC to only take assignments…

Clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) have transformed genome engineering techniques. Numerous toolsets have been created to enable easy and efficient loss-of-function perturbations of functional genomic sites. Study: CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells. Image Credit: elenabsl/Shutterstock The CRISPR/Cas9 system’s elements…

“Over the past few years, with the pandemic, our anxious amygdala, the part of the brain that recognizes danger and puts us on high alert, has been on hyperalert, triggering a near-constant stress response” (Dmitry Kostyukov/The New York Times ) When Jennifer Heisz She was in grad school, borrowed a…

Hi All, I am trying to make cnet plots of differentially expressed genes between 2 tissue types, looking at specific pathways identified from enrichGO analysis. When I plot this a bunch of non-significantly regulated genes are appearing as uncolored dots and I am not sure how to stop this from…

Why did I achieve shorter than initial reads subset after aligned reads extraction. 1 Hello dear colleages! I have recently faced some problem. I have worked with long WGS reads. Firstly I have filtered the longest subset of reads, and aligned them to the custom sequence with several structural variants…

Minimap2 options for Nanopore cDNA direct seq 0 Hello, I’m working with ONT RNA seq data and I used the cDNA direct seq to do the seq. I want to look for long deletions in mRNAs that are not spliced, for this, I want to use the splice option of…

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

Cluster Profiler output not the same as Enrichr output 0 @angkoo-23537 Last seen 18 hours ago United Kingdom Hi there, I have am getting different outputs after running enrichGO on cluster profiler when I put the same genes into enrichR (by Maayan Lab) website. Example here using Biological Process 2021…

find_te_ins is designed to find Transposon Element (TE) insertions using long reads (nanopore), by alignment directly. (minimap2) Install $ git clone github.com/bakerwm/find_te_ins.git
 $ cd find_te_ins Change the following variables upon your condition: genome_fa and te_fa in line-10 and line-11; $ bash run_pipe.sh run_pipe.sh Prerequisite minimap2 – 2.17-r974-dirty, align long…

The Telomere-to-Telomere Consortium is sequencing whole chromosomes.Credit: Adrian T. Sumner/SPL From gene editing to protein-structure determination to quantum computing, here are seven technologies that are likely to have an impact on science in the year ahead. Fully finished genomes Roughly one-tenth of the human genome remained uncharted when genomics researchers…

The program align.py uses mappy to align reads in Python using multiple worker threads. After loading the index the memory usage jumps up quickly to >20Gb and then continues to climb steadily through 40Gb an beyond. This issue was first discovered in bonito and isolated to mappy. The data flow…

Samtools flagstat 1 I aligned my ONT sequencing run with minimap2, subsequently I filtered the file using samtools view -b -F 256 aln_transcriptome_sorted_6.bam -o filtered_aln_transcriptome_6.bam to end up with primary alignments only. When I run samtools flagstat on the filtered file I get the following output: 3502608 + 0 in…

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Finding fuzzy seed matches enable BLEND to find both 1) exact-matching seeds…

ONT analysis on Ubuntu 0 Hello guys, I am new on bioinformatic analysis of data from ONT (MinION with FLOW-MIN106D). The lab sent me a collection of fast5 files I have to analyze to obtain the metagenomic details (viruses). I have the new machine with on board Ubuntu 21 (Nvidia…

TLDR: Thanks to funding from EOSC-Life, the Freiburg Galaxy team will work in 2022 with Biolytix, a Swiss Small and Medium-sized Enterprise (SME) specialized in molecular biology and microbiological analyses, toward Accessible and scalable detection and identification of foodborne pathogens. Background Food contaminations with pathogens are a major burden on…

What is the workshop about? The goal of this course is to provide an overview of in-field, real-time nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform. This course will cover experimental considerations, sample collection and preparation theory, plus data analysis and visualisation. Hands-on opportunities for data analysis of metagenomic…

Mapping multiples 1 Hi, I am coming to you for help. I am doing a mapping on short and long read files with BWA and MINIMAP2 My problem is that, I want to make an if loop that would allow me to choose either BWA if I work with short…

Team Lead Computational Biology in Immunology & Respiratory – Germany Do you have experience in leading a team of computational biologists in immunology & respiratory? If so, then we have the perfect opportunity for you! One of our most highly respected pharmaceutical clients is now looking for a team leader…

COVID-19 laboratory screening Nasopharyngeal/Nasal/Oropharyngeal swabs in viral transport medium (VTM) received from acute phase patients with defined symptoms, asymptomatic cases with contact history with positive patients/ travel history were processed for laboratory confirmation of SARS-CoV-2 at Defence Research and Development Establishment, (DRDE) Gwalior, M.P., India. These samples were referred for…

DNA sequencing has helped develop various sectors of the economy and mainly in the health sector. DNA sequencing has helped scientists understand the causes of related genetic disorders and how to cure them. DNA sequencing has also helped scientists understand the evolution of different animal species. What about developing GMOs?…

Stochastic Amplicon Ligation. DNA samples for oncology sequencing are typically extracted from FFPE tissues and can have average lengths of less than 500 nt due to accumulated chemical damage [18]. We developed the Stochastic Amplicon Ligation (SAL) method to enzymatically concatenate many short DNA molecules together to utilize the long-read…

I am trying to replicate the mergeByOverlap function from R BioConductor in python using the pyranges package. In R the code would be: gr.snp <- with(gr.snp, GRanges(chr, IRanges(start, end),rsid=gr.snp$rsid)) snp.annotated <- data.frame(mergeByOverlaps(gr.snp, gencode, maxgap=2000, type=”start”)) which returns: nrow(snp.annotated) [1] 34 colnames(snp.annotated) [1] “gr.snp.seqnames” “gr.snp.start” [3] “gr.snp.end” “gr.snp.width” [5] “gr.snp.strand” “gr.snp.rsid”…

Feasibility of genomic skimming on the ONT minION sequencer The term ’genomic skimming’ was first coined by in 2012 by Straub et al. (2012)20 as a way to utilize shallow sequencing of gDNA to obtain relatively deeper coverage of high-copy portions of the genome, including mitogenomes. In combining genomic skimming…

Team Lead Computational Biology in Immunology & Respiratory – Germany Do you have experience in leading a team of computational biologists in immunology & respiratory? If so, then we have the perfect opportunity for you! One of our most highly respected pharmaceutical clients is now looking for a team leader…

How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome 0 Hi, I have simulated a set of ONT long reads (10x) of E coli using the Badreads simulator tool. I was wondering is there any way I can know the co…

MinION Data Examples (FAST5) Database 0 Hello everyone, I am constructing a pipeline to analyze Oxford Nanopore MinION data. I have start from FAST5 files and for some optimizations I will try multiple tools for each step. So I will need several datasets to try. As I see most of…