Tag: QC

Job Description Introduction The Outreach and Research Programme of the Department of Paediatrics and Child Health has ten community-based field sites across Pakistan (including four in Karachi) and focuses on research for betterment of women and child health. The Department has a Nutritional Research Laboratory as well as an Infectious…

I have this wrappers in my snakemake file rule fastqc: input: “reads/{sample}_trimmed.fq.gz” output: html=”qc/fastqc/{sample}.html”, zip=”qc/fastqc/{sample}_fastqc.zip” # the suffix _fastqc.zip is necessary for multiqc to find the file params: extra = “–quiet” log: “logs/fastqc/{sample}.log” threads: config[“resources”][“fastqc”][“cpu”] conda: “envs/qc.yaml” wrapper: “v1.31.1/bio/fastqc” qc.yaml: name: qc channels: – bioconda dependencies: – python – fastqc…

Axle Informatics is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations around the globe. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques…

Funding Support and Acknowledgements: COPDGene: The project described was supported by Award Number U01 HL089897 and Award Number U01 HL089856 from the National Heart, Lung, and Blood Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Heart, Lung,…

Position Title: Bioinformatics Scientist Company: AstraZeneca Location: Cambridge, England, United Kingdom Job Description: It propels each of us forward, harnessing our differences to unlock challenges and bring new solutions. Unleash your curiosity and entrepreneurial spirit to uncover new insights that challenge conventions. Here we are forever pushing the boundaries as we feel comfortable…

uBriGene has years of experience in developing cell therapy products, manufacturing GMP cell therapy products and well-rounded QA and QC systems to meet regulatory requirements. We provide clients with CDMO services such as stem cell production technique development, manufacturing, quality testing, and IND application documentation. We provide one-stop services including…

Job Description Job Description and title: Bioinformatics analyst 3 month contract with possibility of extension Typically between 9AM-5PM Central Time. We have an exciting contract opportunity for a Bioinformatics analyst/programmer to support the Emerging Technology Group in GRC. Primary responsibility include providing analysis support for running standard pooled CRISPR screening…

Job Family : Scientific Research & Analysis (Digital) Travel Required : None Clearance Required : Ability to Obtain Public Trust What You Will Do : Provide programming and troubleshooting support to the program in the dissemination of research data. Perform computational data analysis and data management. Work closely with staff…

Mini Review – Journal of Brain and Neurology (2023) Volume 6, Issue 2 Harry Warner* Department of Neurosciences *Corresponding Author: Bin Kayano Department of NeurosciencesUniversity of ExeterUnited KingdomE-mail:h.m.warner@exeter.ac.uk Received:24-Apr-2023, Manuscript No. AAJBN-23-97950; Editor assigned:27-Apr-2023, PreQC No. AAJBN-23-97950(PQ); Reviewed:11-May-2023, QC No. AAJBN-23-97950; Revised:15-May-2023, Manuscript No. AAJBN-23-97950(R); Published:22-May-2023, DOI:10.35841/ aajbn-6.2.146 Citation: Warner…

Bioinformatics Lead Newton, MA (remote ok) Our Client is a Series A, pre-commercial, biotechnology company committed to saving lives through the early detection of cancer. They are looking for a passionate individual to lead Computational Biology for their R&D organization. This individual will play a critical role in the development…

Job Description To discuss more about this job opportunity, please reach out to Chitrank Rastogi (LinkedIn URL – www.linkedin.com/in/chitrank-rastogi-55119a102/), email your updated resume at Email – chitrank.rastogi@collabera.com or give me a call at (425) 523-1648. Thank you! Job Description:Job Roles & Responsibilities: We have an exciting contract opportunity for a…

Single-cell and single-nucleus RNA sequencing of sarcoma subtypes In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing sarcoma (ES), and desmoplastic small round cell tumor (DSRCT) (Fig. 1). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ…

PacBio Pipeline and Tools for Variant Call 0 Hi, I am new to long read seq, I am trying to call Variants on GIAB Trio samples from PacBio data Initially i Aligned reads with Pbmm2 tool, then variant call by DeepVariant 1.5, Phasing through Whatshap. My queries are as follows…

Spectronaut® 18 makes DIA proteomics projects more efficient and scalable than ever for all mass spectrometry instrument types Novel research with TrueDiscovery™ and TrueTarget™ demonstrates the unique capabilities and utility of mass spectrometry proteomics for biomarker and drug discovery Biognosys’ iRT Kit is recommended for real-time system suitability monitoring in…

Job ID: req3395Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: Frederick: ATRFLocation: 8560 Progress Dr, Frederick, MD 21701 USAThe Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc. The lab addresses some of…

At Aldevron, we shape the future of medicine by advancing science in meaningful ways. Our team of dedicated, forward-thinking associates share this goal by combining best-in-class products and service with the ideal operating environment to lay the groundwork for vital new discoveries worldwide. We believe people are our most valuable…

The soil samples were collected from an orchard situated in Karnataka, India, which were categorized based on their stage of infection (ISI, ASI) and compared with a healthy sample (HSC). Physical examination of the plants, with respect to their roots, leaves, stem and fruits, revealed the presence of root knots…

Edit September 5, 2019 NB – this original answer is for 1-colour (channel) Agilent data. Another generic pipeline for 2-colour Agilent is here: A: build the expression matrix step by step from GEO raw data ————— Limma can be used to process Agilent microarray data. Assuming that your data is…

Title- Bioinformatics Analyst Duration-3months with extension Location-Remote   Description: We have an exciting contract opportunity for a Bioinformatics analyst/programmer to support the Emerging Technology Group in GRC. Primary responsibility include providing analysis support for running standard pooled CRISPR screening data and differential expression analysis of bulk RNAseq data, and performing…

Hi , I’m trying to do analysis of chipseq data . I have 3 samples Sample1 , sample2 and input I have done QC and then alignment using Bowtie . After that I used samtool to get bam files . Then I have used Picard for duplicate removal. Now I…

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…

About inconsistent cell counts per samples obtained in small nuclear RNAseq data. 0 Hi, I have single cell small nuclear RNAseq data with inconsistent number of nuclei detected per samples ranging from 250 to 18100 with average count being 5220. So, my question is how we can process these data…

“Applicants must be authorized to work for ANY employer in the U.S. We are unable to sponsor or take over sponsorship of an employment Visa at this time.” Remote 3 month contract with possibility of extension We have an exciting contract opportunity for a Bioinformatics analyst/programmer to support the Emerging…

Bioinformatics Analyst 3 month initial contract with a great possibility of extension. 100% remote position $57 – $60 per hour based on location (medical benefits included) Orion Group and our largest US client are in need of a fully remote Bioinformatics Analyst ASAP!!! Don’t pass on this amazing opportunity! Purpose:…

PLINK not converting entire vcf to bed file 0 here is my code : [ethan.kreuzer@hydra1 2_Population_stratification]$ plink –vcf ALL.2of4intersection.20100804.genotypes.vcf.gz –make-bed –out ALL.2of4intersection.20100804.genotypes [mii] Please select a module to run plink: MODULE PARENT(S) 1 plink/1.9b_6.21-x86_64 StdEnv/2020 2 plink/1.07 nixpkgs/16.09 intel/2018.3 3 plink/1.9b_5.2-x86_64 nixpkgs/16.09 4 plink/1.9b_4.1-x86_64 nixpkgs/16.09 Make a selection (1-4, q…

Annotation of short-read scRNA-seq data with isoform-level information Using fluorescence-activated cell sorting (FACS), we isolated the Lineage-negative, cKit (Cd117) positive (LK) cell fraction of mouse bone marrow cells, a population containing stem and progenitor cells14 from young (8 weeks old, n = 3) and aged (72+ weeks old, n = 3) mice. We generated…

I would run the following code for multiple fastq files in a folder. In a folder I have different fastq files; first I have to read one file and perform the required operations by activating the miniconda , then store results in a separate file. fastq and then read second…

Location: Lake County, IL Contract Length: 3 months (Possible Extension) Pay Rate: $50 – $55 Bioinformatics Analyst Primary responsibility include providing analysis support for running standard pooled CRISPR screening data and differential expression analysis of bulk RNAseq data, and performing standard validation/QC analysis for data generated by the Genome Technology…

Job Description Job SummaryWe are looking for a Research Associate (Post Doctorate) who is interested in joining our DNA data storage and London Biofoundry teams to pursue a PostDoc in the area of next-generation DNA synthesis and sequencing technologies with a particular focus DNA data storage, i.e., on how to…

1Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China; 2Department of Clinical Laboratory, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China Correspondence: Qian Chen, Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China, Tel +8618951768213, Email [email protected]…

Sunrise System Inc. is currently looking for Bioinformatics Data Scientist in Lawrenceville, NJ with one of our top clients. Job Title: Bioinformatics Data ScientistJob Id: 23-04105Location: Lawrenceville, NJ 08648Duration: 12 monthsPosition Type: Hourly contract Position (W2 only) Note: 50%Onsite Job Description: Senior Research Scientist, Disease Strategy and Late Stage Hematology, Translational Bioinformatics 5+ years of…

May 24, 2023 | The Association for Molecular Pathology releases recommendations for germline variants detected by NGS, 10x Genomics wins German injunction against NanoString Technologies, and Revvity—formerly PerkinElmer—announces new license agreement with AstraZeneca. Plus new products and deployments from DNA Script, Thermo Fisher, Model N, GenScript, and more. Clear Labs…

Sunrise System Inc. is currently looking for Bioinformatics Scientist in Lawrenceville, NJ with one of our top clients. Job Title: Bioinformatics Scientist Job Id: 23-04105 Location: Lawrenceville, NJ 08648 Duration: 12 months Position Type: Hourly contract Position (W2 only) Note: 50%Onsite Job Description: Senior Research Scientist, Disease Strategy and Late…

TRANSLATIONAL BIOINFORMATICS RESEARCH SCIENTIST LAWRENCEVILLE, NJ 5+ years of bioinformatics data analysis experience in the Cancer Research setting or Biopharma space 50% onsite/50% remote Required Skills: Ph.D. Or M.Sc. With 3+ years of experience- in computational biology, bioinformatics, biostatistics, or another relevant field. Experience in cancer research institutions, biotech or…

Position Title: Bioinformatics Scientist Company: AstraZeneca Location: Congleton, UK Job Description: This role is within the Centre for Genomics Research. We are looking for recent graduate bioinformatics scientists to support the growing genome analytics and informatics needs of the Centre. You will join the Multi-Omics Data Operations Team and contribute with your bioinformatics expertise to the CGR’s multidisciplinary research…

Hi-Throughput DNA Isolation LGC oKtopure The oKtopure™ is a fully automated nucleic acid extraction platform that combines high-throughput automation with the proprietary sbeadex™ magnetic bead based extraction chemistry for high quality, high yield extraction. Key to the delivery of consistently high quality and high yield DNA preparations from the oKtopure…

A discussion recently arose about how one ought to filter MAPQ in a clinical setting, i.e., where a NGS sample is being processed in order to produce a result for a patient who has an unknown or hypothesised diagnosis. The result could obviously be key. It was suggested by a…

SUMMARY The Genetics Department is a basic science department located in the George and Cynthia Mitchell Basic Sciences Research Building at the world-renowned University of Texas MD Anderson Cancer Center in the heart of the Texas Medical Center. The focus is on advancing knowledge of the molecular genetic mechanisms that…

Current EmployeesIf you are a current Staff, Faculty or Temporary employee at the University of Miami, please click here to log in to Workday to use the internal application process. To learn how to apply for a faculty or staff position using the Career worklet, please review this tip sheet.Transforming…

The MiSeq is an integrated instrument that performs clonal amplification, genomic DNA sequencing, and data analysis with base calling, alignment, variant calling, and reporting in a single run. The MiSeq benchtop instrument utilizes a double-sided, single-lane flow cell and reagent cartridge supplied in kit form. Sequencing is performed by recording…

Study Identification Unique Protocol ID: CNBG 2021001 Brief Title: Clinical Trial on Sequential Immunization of Recombinant COVID-19 Vaccine (CHO Cells) and Inactivated COVID-19 Vaccine (Vero Cells) in Population Aged 18 Years and Above Official Title: Clinical Trial on Sequential Immunization of Recombinant COVID-19 Vaccine (CHO Cells) and Inactivated COVID-19 Vaccine…

Calculating QC Statistics Statistics: Alternative allele frequency > 0.5 sites: 337,476 Reference Overlap: 38.98 % Match: 5,762,722 Allele switch: 0 Strand flip: 0 Strand flip and allele switch: 0 A/T, C/G genotypes: 0 Filtered sites: Filter flag set: 0 Invalid alleles: 0 Multiallelic sites: 63,834 Duplicated sites: 21 NonSNP sites:…

Posted by hagansa2 on Wednesday, May 17, 2023 in Job Opportunities . Bioinformatics Scientist will be responsible for assisting research and development team in a collaborative and multi-disciplinary effort in developing and validating OmniSeq’s molecular diagnostic and next generation sequencing based bioinformatics analysis pipelines, along with playing an important role…

This course will provide training on RNAseq data production and interpretation. The course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. We will dedicate some time to analysing and constructing networks from…

Inference of HLA-I tumor status with LILAC. a, Representation of the six immune escape pathways considered in the present study alongside their associated genes (adapted from ‘MHC class I and II pathways’, by BioRender.com). The genes considered for each immune escape pathway are depicted in gray. b, Left, workflow of…

Hi, I’m download some datasets from Geo Database (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155960) I found the names are in ENSEMBL nomenclature and I need to convert into Gene symbol in order to do the QC metrics in the Seurat pipeline. I’m using this code to convert the ENSEMBL to gene symbol: library(Seurat) library(patchwork) library…

Job Description: If you are looking for a company where you can gain exposure to a wide variety of science and explore a multitude of career paths across the drug development spectrum, consider working at Labcorp Drug Development as a Bioinformatics Scientist I (Prod). In this role, you will join…

1. Introduction 2. Basic information 3. Downloads and general notes 4. Command reference table 5. Basic usage/data formats 6. Data management 7. Summary stats 8. Inclusion trim 9. Population stratification 10. IBS/IBD estimation 11. Bond 12. Family-based community 13. Permutation process 14. LD calculations 15. Multimarker tests 16. Conditional haplotype…

Animal rearing and samples collection Our experiment was designed to compare eight female Laiwu pigs (LW) with eight female Lulai pigs (LU) which crossbred between LW and Yorkshire breeds. All pigs were born and raised for approximately two years (715 ± 33 days, Table 1) under uniform housing and feeding conditions at Jing-Qi-Shen…

Perspective – Journal of RNA and Genomics (2023) Volume 19, Issue 2 Stephen Finnie* Department of Genetics, University of Adelaide, Adelaide, Australia Corresponding Author: Stephen FinnieDepartment of Genetics,University of Adelaide,Adelaide, AustraliaEmail: stephenfinnie@gmail.com Received: 15-Feb-2023, Manuscript No. RNAI-23-95180; Editor assigned: 17-Feb-2023, Pre QC No. RNAI-23-95180(PQ); Reviewed: 03-Mar-2023, QC No. RNAI-23-95180; Revised:…

Permanent/Full time, London or Cambridge, UK Hybrid working options available. About Us: Join the multiomic revolution! Over the last 20 years, genomic technologies have enabled significant discoveries that bring the promise of personalized medicine closer than ever before. But after two decades of research, it’s clear that genetic variation only…

Us Seed Health is a microbiome science company pioneering innovations in probiotics and living medicines to impact human and planetary health. Our scientific board comprises leading scientists, researchers, and clinicians across the fields of microbiology, immunology, bioinformatics, dermatology, oral health, vaginal health, gastroenterology, mental health, pediatrics, and nutrition.  Consumer innovations…

Be among the first applicants. System One Nutley (New Jersey) USD 80,000 – 100,000 Today Job description Title: Bioinformatics ScientistLocation: Nutley, NJDuration: 12-monthsSchedule: M-F Full TimeTarget Start Date: ASAP Responsibilities: Provide bioinformatics support on one or more project team(s) in translational science, and early/late phase cancer clinical trials, accountable for…

By Dr Ryan Roberts, cell processing lead at Cellular Origins Despite the rapidly emerging innovations in the field of cell and gene therapy, bottlenecks in cell therapy manufacturing processes are preventing these transformative medicines from reaching patients. There are several broad challenges to the scalability and affordability of cell therapies,…

Genialis, a computational precision medicine company unraveling complex biology to find new ways to treat disease, today released Genialis(™) Expressions version 3.0 to accelerate translational and clinical biomarker discovery. Expressions is a platform for the analysis and management of sequencing data that makes data querying and processing faster, smarter, and…

We are seeking a bioinformatician with significant oncology or immunology experience to join a multidisciplinary team developing leading-edge genomics analysis tools to understand the immune system’s response to cancer. This highly motivated, detail-oriented individual would join a clinical genomics analysis group and will be responsible for developing and applying bioinformatics…

Low % reads mapped and high % genome coverage 1 Bacterial isolate sequenced on Illumina platform, fastq’s are decontaminated prior to mapping and alignment. Coverage analysis run with samtools and then mapping stats calculated with mapped reads count text file vs total reads count text file. I have a sample…

This protocol provides a rapid and size-specific isolation method for small extracellular vesicles by optimizing the size of the air spray nozzle, sheath fluid pressure, sample flow pressure, voltage, gain, and triggering threshold parameters. This protocol provides a rapid and size-specific solution method for small extracellular vesicles by optimizing flow…

High number of duplicates and low percentage properly paired 0 I have some paired end sequencing data that I have trimmed using cutadapt. It was sequenced on an illumina novaseq 6000 and is low coverage RADseq data (2-3x). My cutadapt script used forward and reverse adapters from illumina : cutadapt…

Hi everyone, I have 2 samples, paired end RNA sequence from illumina. I have done the QC and trimming. now after triiming with trimgalore I have A_R1.val_fq A_R2.val_fq B_R1.val_fq B_R2.val_fq Now I performed tophat for genome mapping. I ran this command tophat -p4 -G GRCh38_latest_genomic.fna -o tophat_result bowtie_index A_R1_val.fq but…

I extracted three samples (HG02024 – HG02026) from the 1000 Genomes Project’s 30x alignment files, employing the Genome Analysis Toolkit (GATK) best practice pipeline. This process involved performing base quality score recalibration, identifying and removing duplicate reads, utilizing the HaplotypeCaller to generate a genomic VCF (gVCF) file, and calling variants…

Bioinformatics Analyst II Job ID: req2894Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: Frederick: ATRFLocation: 8560 Progress Dr, Frederick, MD 21701 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc. The…

Amidst the slow but steady growth, India has a long road ahead to become a master in the NGS market India is making huge strides in the next-generation sequencing (NGS) market. It has to be remembered that the sequencing of the SARS-CoV-2 has helped to develop vaccines in record time,…

Plant material Streptocarpus grandis (RBGE lineage 19771210) and Streptocarpus kentaniensis (RBGE lineage 19951992) were cultivated in the glasshouses at the Royal Botanic Garden Edinburgh. DNA extraction method for Streptocarpus PacBio HiFi long-read sequencing To develop the protocol, small scale extractions were carried out with approx. 3 g leaf tissue as input…

Dataset Description Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. This cohort comprises a subset of patients enrolled in the Genomic Advances in Sepsis (GAinS) study, an established biobank of adult sepsis patients. Patients with sepsis due to community acquired pneumonia or faecal…

Human CD34+ cell isolation Human fetal liver (FL) samples were obtained from Advanced Biosciences Resources (Alameda, CA) with proper consent. FL samples were cut in small fragments, treated for 25 min at 37 °C with Collagenase D (100 ng/mL; Roche). The cell suspension was prepared, and the human CD34+ cells were separated by…

Study cohort and performance during NMP An overview of the overall study population is presented in Table 1 (individual data are given in Supplementary Table 1). Detailed information on study livers and analysis is provided as workflow scheme in Fig. 1. The decision to apply NMP was based on one or a combination…

Low percentage of ‘Fraction Antibody Reads Usable’ in Feature Barcode Cell Ranger output 0 Hi, I have a question regarding the Cell Ranger output of scRNAseq with Feature Barcode. I’ve performed the standard Cell Ranger count using cellranger-6.0.0 and the following arguments: –id=A_GEX –libraries=library_A.csv –transcriptome=/……/refdata-gex-GRCh38-2020-A –feature-ref=/…../10x_feature_ref.csv When looking at the…

All experimental procedures described in this manuscript were carried out in accordance with relevant guidelines and regulations including biosafety and chemical safety regulations. All nucleic acid sequences used were obtained from publicly available NCBI/GenBank collections and no human subject research was conducted in the course of this project. No materials…

Edit November 28, 2020: Further reproducible code: A: GPL6883_HumanRef-8_V3_0_R0_11282963_A (illumina expression beadchip) — Most Illumina ‘chip’ studies that I have seen on GEO do not contain the raw data IDAT files. You can start with the tab-delimited file, but will also require the annotation file (contained in the *_RAW.tar file),…

A total of 47 SARS-CoV-2 positive samples with real-time PCR Ct values ranging from 14 to 30 were sequenced with three different protocols for SARS-CoV-2 sequencing, involving enrichment by bait hybridization or tiled amplicons. A schematic overview including library preparation, target enrichment, and sequencing is shown in Fig. 1. All 47…

Combination of PacBio’s HiFi Sequencing Capabilities and Form Bio’s Computational Platform and Solutions Helps Biopharma and Academic Researchers Innovate and Accelerates Gene Therapy Product Development DALLAS, April 19, 2023 (Newswire.com) – Form Bio, the provider of advanced computational life sciences technology, today announced it has joined the PacBio Compatible program….

Hi, I’m running a big SNP database (160GB vcf file) I pruned with plink; plink –vcf SNPs_clean1.vcf –allow-extra-chr –indep-pairwise 50 10 0.1 –out SNP_50_10_01 It starts running producing the temporary files and the output files prune.in and prune.out). In the log file it shows having filtered the variants, 49595998 of…

Apply hard-call-threshold to pgen files using PLINK2 1 Hi, I am doing QC to the UK biobank imputed genotype data (in pgen format) using PLINK2. One of the QC criteria is –hard-call-threshold .05. There is no indication in the .log file on the number of variants removed because of this…

16S FASTQC report and removing over represented and duplicate sequences. 0 I have 16s data the attached is the QC report shows some errors should I need to remove overrepresented sequences? I did it using fast P but keeping the default parameter P=20 but it did not make any change…

Back to Bioinformatics Main Menu Evaluation FastQC GCATemplates available: grace terra module spider FastQC After running FastQC via the command line, you can ssh to an HPRC cluster enabling X11 forwarding by using the -X option and view the images using the eog tool. From your desktop: ssh -X username@grace.hprc.tamu.edu From your FastQC working…

Why is Beagle v5.4 (imputation) not giving Allele Frequencies (AF) and DR2 in my output? 0 Hi there! I have just imputed some low-coverage (<4x) whole genome sequencing samples using a WGS reference panel (>10x) and Beagle v5.4: java -jar beagle.22Jul22.46e.jar gt=${file} impute=true gp=true ne=100 nthreads=16 ref=${refvcf} out=${outfile} However, the…

Analysis a scRNAseq object that already has cell type annotation 0 Hi all I have recently downloaded a publicly available scRNAseq dataset that I want to analyse. The goal will be to do some differential expression analysis between two specific cell type clusters. The raw file was in .h5ad format,…

Scientist III- Computational Biology Ridgefield, CT12 month W2 contract (with potential to extend or transition to perm)Pay rate: $40-48/hour Some of the Your Responsibilities: Strong scientific understanding and experience in bioinformatics Experience in pharmaceutical research a plus Design, implement and/or deploy NGS data analysis workflows for data processing, visualization, integration…

single cell multi-modal data (CITEseq) batch correction 0 I’m working with a BD Rhabsody AbSeq data set containting a targeted scRNA and surfce protein (ADT) layer measured in two batches. In general I aim to integrate both modalities (e.g. MOFA+ or SeuratV4) for a joined analysis. While I perform QC…

Bioinformatics Analyst II Job ID: req2894Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: Frederick: ATRFLocation: 8560 Progress Dr, Frederick, MD 21701 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc. The…

trimmomatic and STAR alignments 0 Hi! I was wondering if anyone knows what the current best practices are for QC and trimming sequencing bulk RNA-seq reads before aligning them to a reference genome. I was motivated by reading about how STAR works (finding a seed within each read that matches…

Calculating fold 80 base penalty by hand 0 Hello, Is there a simple formula for calculating fold 80 base penalty without using Picard metrics? For example using knowledge about number of sequenced bases, mean coverage and standard deviation of mean coverage of WES experiment? metrics Fold QC Picard 80 WES…

Demographic characteristics of sampled patients The Uganda Virus Research Institute National Influenza Centre (UVRI-NIC) laboratory tested 18,353 patients between 22nd October 2010 and 9th May 2018. Thirteen-percent (2404/18,353) were positive for influenza, 69.88% (1680/2404), 29.62% (712/2404), and 0.17% (4/2404) had influenza A, B, and A/B co-infection, respectively (Fig. 1A). IAV positives…

I am getting the following output after running Plink. Why am I getting the following warning for some SNP markers? I have checked those markers, they are not triallelic. Then where is the error? How can I fix it? Scanning .ped file… Possibly irregular .ped line.  Restarting scan, assuming multichar…

I’m working with SN RNA-seq data that I processed using Cellranger v. 7.1.0 (which uses STAR for alignment with default settings). Using the samtools flagstat command to look at a BAM file output: 284890368 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0…

Low featurecounts assignment rate 0 Hi all, I am currently running QC, trimming, and alignment steps on bulkseq RNA mouse samples (lung from diabetic vs. wildtype). For each sample, I received R1 & R2 reads. The alignment runs alright, but once I put the sorted BAM files into FeatureCounts I…

I am working DESeq2 i wanted i proper boxplot but i don’t understand what wrong i am doing and i wanted to know how to properly plot the x and y axis what parameters should be taken for boxplot . here’s my code: library(“DESeq2”) library(“ggplot2”) counts<-read.delim(“PC_1.csv”,header = TRUE, row.names =…

The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group established in 2016, with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient samples. Led by director, Simon Gayther, PhD, the primary goals of the CBFG are to…

Any methods available to do QC analysis of Pacbio raw data?? 3 Hi, I am very new to NGS. Am going to have pacbio raw data in few months. What am looking for is, methods to verify and validate the raw data. I want to find out how good is…

Nextflow rnaseq finishing early 0 Hi I’m running the RNA-seq pipeline from nextflow and I have been running it without problems until this dataset it just stops prematurely saying it has finished when it doesn’t even aligns the reads with salmon. Any ideas what may be going on? I have…

Trajectory analysis using Monocle3 with Seurat sub-clustering 0 Hi all, I am analyzing single cell RNA-seq data using Seurat and trying to do trajectory analysis using Monocle3. My analysis pipeline is below. # QC, NormalizeData, FindVariableFeatures for each sample independetly SelectIntegrationFeatures > FindIntegrationAnchors > IntegrateData > > ScaleData > RunPCA…

Michigan Imputation server failed job 0 This is the first time I use Michigan Imputation Server. My imputation worked as it should on all chromosomes (1 to 22) apart from chromosome 9, where the job starts and then it fails and I don’t know why and how to fix this…

The oligo duplex synthesis service allows to obtain a fragment of dsDNA up to 220 bases long, not cloned, carefully controlled and in such quantity as to be used for a large number of applications. The service includes: synthesis, purification and QC (HPLC and Mass Check) of two complementary DNA…

Hello everyone I am working on spatial transcriptome data. I am following some tutorial (nbisweden.github.io/workshop-scRNAseq/labs/compiled/seurat/seurat_07_spatial.html#Subset_ST_for_cortex) for the QC, normalization and integration of multiple samples. After all analysis, I am interested in generating the feature-plot of desired set of genes. I used following two approaches : brain1 <- LoadData(“stxBrain”, type =…

Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ? 0 Hi, I don’t know much about bioinformatics and R language, I just know how to use some bioinformatic tools in a simple way. That´s why I prefer to follow simple tools to analyze my Illumina seqs…

Fastqc lsequence duplication and per base sequence content failed 1 I have around 150bp, paired-end RNA-seq data of 321 samples with around 30 Million reads per sample and I am interested in quantifying the expression for the transcriptome-wide association studies (TWAS). I have performed QC using fastqc. The per base…

Post-Imputation QC Problem 0 I’m struggling with post-imputation processing of some data, and I would be very grateful for some guidance. I have a data set that has been imputed through Michigan Imputation Server. I now need to perform post-imputation processing. I’ve attempted to run the data through Plink with…

mRNA Seq 0 I have done mRNA sequencing and i got fastq data, but only Read 1 are aligning to reference genome and R2 is not aligning. Its not proper R1 and R2 alignment. But library qc is fine. Please let me know about read alignments and why is that…

NEW YORK – UK biotech company Touchlight is using its proprietary in vitro DNA production platform to manufacture doggybone DNA (dbDNA), an enzymatically amplified DNA vector that the company said is a more scalable alternative to traditional plasmid DNA. While the Hampton-based contract development and manufacturing organization (CDMO) is currently…