Tag: NovaSeq

Head of bioinformatics – Lausanne

Head of bioinformatics Introduction UNIL is a leading international teaching and research institution, with over 5,000 employees and 17,000 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility. The Lausanne Genomic Technologies Facility (GTF) is a service platform working for…

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Protocols

normalization data transformation protocol 10X Genomics Visium sequencing data were aligned and quantified using the Space Ranger Software Suite (version 1.0.0, 10x Genomics Inc) using the GRCh38 human reference genome (official Cell Ranger reference, version 3.0.0). Spots were manually aligned to the paired H&E images by 10x Genomics. nucleic acid…

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A genomic mutation spectrum of collecting duct carcinoma in the Chinese population

This article was originally published here BMC Med Genomics. 2022 Jan 3;15(1):1. doi: 10.1186/s12920-021-01143-2. ABSTRACT BACKGROUND: Renal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In…

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Benchmarking the NVIDIA Clara Parabricks germline pipeline on AWS

This blog post was contributed by Ankit Sethia, PhD, and Timothy Harkins, PhD, at NVIDIA Parabricks, and Olivia Choudhury, PhD,  Sujaya Srinivasan, and Aniket Deshpande at AWS. This blog provides an overview of NVIDIA’s Clara Parabricks along with a guide on how to use Parabricks within the AWS Marketplace. It…

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Single-cell delineation of lineage and genetic identity in the mouse brain

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

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The Biostar Herald for Tuesday, September 21, 2021

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…

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Korea to establish national digital library on health and genome data by 2028

Global next-generation sequencing and technology expert Illumina will assist multi-ministerial project National Project of Bio Big Data in Korea has selected Illumina technology for the second pilot project in their effort to work towards establishing a national digital library on health and genome data by 2028. The multi-ministerial project is…

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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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bash loop to python loop for google colabs

bash loop to python loop for google colabs 1 Hi there, I have a bash loop to use kallisto on my sequencing samples, but I’m trying now to run kb on google colabs (all the fastq files are on Google drive), so I’d appreciate a hand in ‘translating it to…

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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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Picard CalculateHsMetrics perTargetCoverage for Novaseq bams

Picard CalculateHsMetrics perTargetCoverage for Novaseq bams 0 Hello, I would like to use Picard’s CalculateHsMetrics to calculate per target coverage for Novaseq bam files. It seems that the tool is not able to calculate mean/normalized coverage for Novaseq bams but works well with Hiseq bams. Novaseq bams report quality scores…

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Get failed reads on Novaseq

Get failed reads on Novaseq 0 Dear all, on a NextSeq550, I can get failed reads (not PF) with –with-failed-reads using bcl2fastq. With the more modern bclconvert software, this does not exist. support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html Also, it seems failed reads are not saved any more by the Novaseq, which is problematic for…

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Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

. 2021 Sep;39(9):1129-1140. doi: 10.1038/s41587-021-01049-5. Epub 2021 Sep 9. Jonathan Foox  1   2 , Scott W Tighe  3 , Charles M Nicolet  4 , Justin M Zook  5 , Marta Byrska-Bishop  6 , Wayne E Clarke  6 , Michael M Khayat  7   8 , Medhat Mahmoud  7   8 , Phoebe K Laaguiby  3 , Zachary T…

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ABRF Study Benchmarks NGS Platforms on Human, Microbial Samples, Provides Peek at Genapsys Data

NEW YORK – The results of a major, core facilities-driven benchmarking study for next-generation sequencing platforms are in, and just about every major player in the field can claim a victory of some sort. The data support longstanding advantages touted by market leader Illumina, while also providing a sneak peak…

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Bioinformatics Scientist I job in Temple City, CA | Fulgent Genetics, Inc.

ABOUT FULGENT: Fulgent is a leader in genetic and genomic clinical testing, a publicly traded company located in Los Angeles, California. We are a technology-driven company with extensive academic/clinical experience and capabilities in Next Generation Sequencing (NGS) and bioinformatics. This distinction has advanced us to the forefront of the rapidly…

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Interpreting read coverage over gene body plot

Interpreting read coverage over gene body plot 0 Hi, I’m working on some RNA-seq data for my thesis and I was hoping that someone could help me out. My sequencing library was prepared using Illumina TruSeq Stranded mRNA kit and sequenced with a NovaSeq sequencer. After read alignment I did…

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NextSeq 2000 Sequencing | University of Minnesota Genomics Center

The NextSeq 2000 is Illumina’s newest platform that uses advancements in optics, instrument design, and 2-channel chemistry to increase output. This new sequencing technology makes it possible for researchers to sequence a range of conventional and emerging applications by increasing throughput while cutting down on costs per run when compared…

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Advanced genomics research centre inaugurated

Next generation sequencing can bring about a revolution in biological sciences and unprecedented progress to society as genomics is the sunrise sector of the 21st century just like Information Technology in the 90s took the country to great heights, said Defence Minister Rajnath Singh on Thursday. Mr. Singh was speaking…

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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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Combining 2 different depth RNA-seq data (DESeq2)

Hello, I have two RNA-seq data generated from Illumina Novaseq (same experimental design but different depth, 25M and 15M reads/sample for Run1 and Run2 respectively). The dateset look like this: Samples Condition Run Sample_1 A R1 Sample_2 B R1 Sample_3 A R1 Sample_4 B R1 Sample_5 A R1 Sample_6 B…

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Combining RNA-seq data from 2 experiments (DESeq2)

Hello, I have two RNA-seq data generated from Illumina Novaseq (same experimental design but different depth, 25M and 15M reads/sample for Run1 and Run2 respectively). The dateset look like this: Samples Condition Run Sample_1 A R1 Sample_2 B R1 Sample_3 A R1 Sample_4 B R1 Sample_5 A R1 Sample_6 B…

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