Tag: QC

Description The Genome Bioinformatics Analyst works independently to curate disease, gene and variant knowledge including variant interpretation, reporting and consultation with laboratory staff, physicians and genetic counselors. The analyst participates in clinical test development, validation and maintenance of data analysis pipelines, monitoring of quality metrics and the analysis of large…

About the job Our Team: Artificial Intelligence (AI) and Machine Learning (ML) algorithms can significantly speed up drug discovery and shorten drug development and identification of patients for clinical trials thereby creating better medicines that save lives. AI and Deep Analytics (AIDA) is a critical group in Data and Data…

featureCounts paired end reads wrongly assigned on the single end mode 0 Hello! I have RNAseq data from samples containing 2 to 3 bacterial strains each. For the analysis I performed FastQC, trimmomatic to remove adapters and then Bowtie2 to align the reads to the reference genomes. I have one…

Diagnostic innovator TAmiRNA now has in its product pipeline an innovative NGS technology for absolute quantitation of miRNAs and other small RNAs , the miND® (microRNA Next-Generation Sequencing Discovery) spike-in. The miND® spike-in has been developed for small RNA sequencing experiments and absolute quantitation of microRNAs in any biological matrix…

Methylation is one of the most classical epigenetic modifications in eukaryotes. DNA methylation regulates gene expression and has important implications in both growth and disease-related research. DNA methylation affects the maturation of germ cells or embryonic cells subject to specific gene expression. It has also been widely studied and applied…

Changes in ped and map files in PLINK 1 Hello all, I want to do QC with Plink but I want to have the changes of QC in my ped and map files after QC. I used the items below but received .bim, .fam, and .bed files. My ped and…

Choo, L. M., Niissalo, M. A., Leong, P. K. F. & Khew, G. S. The complete plastome sequence of Gordonia penangensis Ridl. supports the transfer of Asian Gordonia into Polyspora (Theaceae). Phytotaxa 458, 159–166 (2020). Nguyet, H. N. L. et al. An updated checklist of Theaceae and a new species…

Not everyone who completes a life sciences PhD wants to continue working in a laboratory or in research. They may just have grown out of it or found that the work isn’t what they thought it was. Or maybe they still love science and would rather find a different way…

10x scRNAseq samples with similar reads/cell but vastly differing UMI/cell 0 Hi all, Been trying to get my had around some discrepancies between a couple of 10x datasets. Both were sequenced to a depth of ~500k reads total and 2-3k cells yielded but then give vastly different UMI/cell as final…

Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US Usman A. Tahir, Daniel H. Katz, Jeremy M. Robbins, Zsu-Zsu Chen, Mark D. Benson, Daniel E. Cruz, Debby Ngo, Shuliang Deng, Xu Shi, Shuning Zheng, Aaron S. Eisman, Laurie Farrell, James G. Wilson & Robert E. Gerszten Broad Institute of Harvard and MIT, Cambridge, MA, US Julian Avila-Pachecho, Alexander G….

Study population The study sample included 34,072 unrelated (3rd degree or less) TOPMed participants from eight U.S. based cohort studies: Jackson Heart Study (JHS; n = 2504), Framingham Heart Study (FHS; n = 3520), Hispanic Community Health Study/Study of Latinos (HCHS/SOL; n = 6,408), Atherosclerosis Risk in Communities study (ARIC; n = 6197), Cardiovascular Health Study (CHS; n = 2835),…

what can cause high(> 80%) spike-ins and low read count (<100 reads) in low complexity ampseq run 1 Hello, I have data output from low complexity ampseq run. The read counts are very low (<100 reads per well) and the spike-ins% is very high (>80%) across all of the samples….

Patrick Murphy Bulk RNA-Seq – HackMD        owned this note   Published Linked with GitHub — title: ‘Patrick Murphy Bulk RNA-Seq’ disqus: hackmd — Patrick Murphy bulk RNA-Seq Analysis === ## Table of Contents [TOC] ## 1. Introduction This is a bulk RNA-Seq project, which includes human data….

Responsibilities Requisition # HRC0992682 The newly formed Precision Biomarkers Laboratories (PBL) at Cedars-Sinai is seeking a highly skilled bioinformatics professional with an expertise in statistical methods and data applications. This role will be responsible for developing robust statistical measures to evaluate, analyze, and integrate proteomics data for continuous quality control…

You will be joining a multi-disciplinary team of bioinformaticians and biologists to tackle the most burning questions of the pharmaceutical industry using cutting-edge data. You will run the pipelines that generate and integrate machine-learning models of the immune system. Disease models are dynamic and constantly improve as data accumulates. These…

This position will be responsible for the continued development and maintenance of RNAseq data analysis and other bioinformatics pipelines. DSRD has invested heavily in our capacity to generate genomic and transcriptomic data, including quickly evolving areas such as single cell RNAseq and spatial transcriptomics. The successful candidate will be responsible…

Everyone’s unique health journey is informed by data. Join us as we translate today’s discoveries into tomorrow’s medicine! Cedars-Sinai is home to some of the most advanced biomedical research and training programs in the world, which attracts renowned physician-scientists seeking an unparalleled environment for fostering invention and teamwork. The Department…

Job Functions, Duties, Responsibilities and Position Qualifications: POSITION TITLE:Senior Bioinformatics-Clinical Database Developer STANDARDIZED JOB TITLE: Database Development, Web Application Development, and Clinical Analytics EXEMPT STATUS:  Exempt POSITION SUMMARY: Sr. Database Developer works with cross-functional groups & Medical Leadership for developing a databases for a clinical assays. The candidate is expected…

Job Description Look for more than answers. At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can…

. 2022 Jun 17;3(3):101491. doi: 10.1016/j.xpro.2022.101491. eCollection 2022 Sep 16. Affiliations Expand Affiliations 1 Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA. 2 Institute for Memory Impairments and Neurological Disorders (MIND), Irvine, CA, USA. 3 Mathematical, Computational and Systems Biology Program, UC Irvine, Irvine, CA, USA….

Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…

Reporting results from fastp Read GC content 1 Hi, I have some QC results for a Paired end seq before and after filtering (Mouse samples). I am unable to interpret the plot Read GC content and I am not sure if the results are fine in this case. I am…

Introduction Lung cancer is associated with high morbidity and mortality and continues to be a major public health problem worldwide (1). Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. While the 5-year survival rates of patients with lung cancer are still <15%, rates are closer to…

Circulating cell-free DNA (cfDNA) is fragmented extracellular DNA, which is released from apoptotic and necrotic cells in small fragments of <200 bp [1]. cfDNA is typically isolated from the blood stream; however, it is also possible to detect cfDNA in other biological fluids such as urine or cerebrospinal fluid [2, 3,…

LA JOLLA, Calif., Feb. 28, 2022 (GLOBE NEWSWIRE) — Singular Genomics Systems, Inc. (Nasdaq: OMIC), a company leveraging novel next-generation sequencing (NGS) and multiomics technologies to empower researchers and clinicians, today announced a partnership with Agilent Technologies (www.agilent.com) to validate its NGS Target Enrichment Products, highly sensitive target enrichment panels…

Read counts an order of magnitude higher on one chromosome 3 Hi, I am having an issue with a sequencing run that when demultiplexed, aligned, and filtered each individual has 1-2 million reads, but these reads are predominantly on one chromosome. For background these are oncorhynchus mykiss and o. clarki…

Bispecific antibodies: rising stars in antibody therapeutics Monoclonal antibodies (mAbs) are important therapeutic agents for the treatment of many human diseases, such as cancer, autoimmune diseases, cardiovascular diseases, asthma, and viral infections. Unlike monospecific mAbs, bispecific antibodies (bsAbs) are antibodies containing two antigen-binding sites and therefore can simultaneously target two…

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…

Help me understand the Nanopore fastqc results 2 Hi, I have got my first Nanopore sequencing data and the first step was to see if the data is good. Has anyone has any experience with this kind of data and can tell me how to interpret the results. The whole…

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

Details Posted: 27-Apr-22 Location: Boston, Massachusetts Salary: Open Categories: Staff/Administrative Internal Number: 2022-26005 Located in Boston and the surrounding communities, Dana-Farber Cancer Institute (DFCI) brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people…

** Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing ** The NeuroGenomics and Informatics (NGI) Center lead by Dr. Carlos Cruchaga at Washington University School of Medicine is recruiting a Bioinformatics Scientist to work on Whole Genome and Whole Exome Sequencing. We are seeking an experienced, self-motivated, self-driven scientist…

Details Posted: 22-Apr-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Leads a team of bioinformaticians and provides technical guidance for the team to follow best practices and deliver data production timely. Collaborates cross-functionally with our user services, software engineering,…

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

Scientists and health officials throughout the world are raising the alarm about the emergence and spread of more COVID variants, subvariants and third generation subvariants with the worrying mutations, which have been linked to increased fusogenicity, illness severity, and death. Infectivity and transmissibility have also grown in these new BA.2 subvariants…

Hi all! I am analysing CSS Pacbio data and each sample came from different run, in particular I have three files for each sample. I tested both pbmm2 and minimap2 to align my long reads, after getting the consensus sequences. This is the command I used to run mnimap2: minimap2…

Respiratory telemetry is a different modality of the pulmonary function testing that is now increasingly used in the clinical and research setting. Oscillometry is conducted through tighter breathing with three acceptable measurements, and can be performed with minimal contraindications. The main advantage of respiratory oscillometry is that it requires minimal…

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I used FaQC to qc my raw fastqs before assembling. That program (and perhaps others) outputs properly paired Forward and Reverse fastqs, as well as an unpaired fastq file for each sample. I used the all 3 for each single sample assembly. Since minimap2 only allows for 2 query files,…

Hi, I was trying to run regenie workflow in ukb rap (part E). github.com/dnanexus/UKB_RAP/blob/main/GWAS/regenie_workflow/partE-step2-qc-filter.sh All the previous steps ran perfectly without any error. But in this step partE-step2-qc-filter.sh I am getting dx: error: unrecognized arguments: –bfile ukb23155_c22_b0_v1 –no-pheno –keep natd_wes_200k.phe –autosome –maf 0.01 –mac 20 –geno 0.1 –hwe 1e-15 –mind…

I wonder if someone please explain what secondary, supplementary, duplicates and paired in sequencing mean in samtools flagstat 0 ”194492 + 0 in total (QC-passed reads + QC-failed reads) 80 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 193804 + 0 mapped (99.65% : N/A) 194412 +…

calculate_condition_mean_sd_per_gene Calculate statistics for each gene of an expression matrix given a grouping crossPanel Generate the cross plot panel of the shiny app crossPanelServer Generate the cross plot panel of the shiny app crossPanelUI Generate the cross plot panel of the shiny app cross_plot Create a cross plot comparing differential…

Bioinformatics Scientist 2 Hours: 37.5 hours per week Salary: Competitive Ref No: HRJOB7442 Business Unit: Diagnostic Services Location: Craigavon or Manchester Open To: Internal and External Applicants The Company Almac Diagnostic Services is a leading stratified medicine business, specialising in biomarker-driven clinical trials. We are incredibly proud to be involved…

Study approval was provided by the Research Ethics Committee of the University of Perugia (report n.2018-21 of 11/12/2018) according to Italian Ministry of Health legislation18. All methods were carried out following relevant guidelines and regulations and the study was carried out in compliance with the ARRIVE guidelines. Informed consent is…

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Alabi RO, Farber G, Blobel CP (2018) Intriguing roles for endothelial ADAM10/Notch signaling in the development of organ-specific vascular beds. Physiol Rev 98:2025–2061 CAS  Article  Google Scholar  Autiero M, De Smet F, Claes F, Carmeliet P (2005) Role of neural guidance signals in blood vessel navigation. Cardiovasc Res 65:629–638 CAS …

Circular RNAs (circRNAs) are a novel class of noncoding RNAs that play important roles in human diseases. However, the regulation of circRNAs in glucocorticoid-induced osteoporosis (GIOP) has not been reported. In this study, we performed high-throughput sequencing to identify altered circRNAs in the vertebrae from GIOP patients. A total of…

Hi everyone, Wondering if someone can provide me with some guidance. I have previously sequenced 4 skin cancers using 10X chemistries and I would like to combine them into one dataset. My research question is to look at cancer stem cell populations, so I will need sensitivity. I have done…

Introduction to RNA-seq data analysis – Extended Materials | cruk-summer-school-2021 Github repo for 2021 CRUK-CC Bioinformatics Summer School (tinyurl.com/crukss2021) Taught remotely Bioinformatics Training, Craik-Marshall Building, Downing Site, University of Cambridge Supplementary materials These files contain some additional information and exercises not included during the taught course. Obtaining public data Raw…

Hi, I am a bioinformatics student and I am struggling with an issue, I had paired-end fastq files for one sample with some low-quality bases at the end and adapter contamination, so I went and I trimmed my reads with trimmomatic, it gave me 4 files that I used for…

I realized that this is a stupid mistake I have made. Since samtools do not overwrite the files by default, the output that I get from samtools merge output.bam f2.bam f1.bam wan’t what I thought it was below is my original post ++++++++++++++++++++++++++ I’m using samtool/1.9.0 and I’m trying to…

Plink Alternative Phenotype File Columns not being Read 0 Hi, I have a plink alternative phenotype file with the following format: FID IID Phenotype 1 2 1 1 3 0 etc. As outlined in the plink documentation. zzz.bwh.harvard.edu/plink/data.shtml#pheno However, when I run the following command : plink –bfile ../Plink_Files/plink –logistic…

DOI: 10.18129/B9.bioc.RiboCrypt     Interactive visualization in genomics Bioconductor version: Release (3.14) R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots….

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

Same issue as mentioned on the minimap2 tool: github.com/lh3/minimap2/issues/236#issue-361097444 For example nanopore reads aligned to the host transcriptome the flagstat output is: 5953480 + 0 in total (QC-passed reads + QC-failed reads) 2961480 + 0 secondary 22696 + 0 supplementary 0 + 0 duplicates 4195469 + 0 mapped (70.47% :…

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…

Incyte is a biopharmaceutical company focused on the discovery, development, and commercialization of novel medicines to meet serious unmet medical needs in oncology and inflammation and autoimmunity. Incyte is committed to the rigorous pursuit of research and development excellence to improve the lives of patients, make a difference in health…

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

RNA-seq analysis cloud server 1 Hi all, I have some RNA-seq of mice (around 200GB) and I want to perform a RNA-seq analysis (including QC, mapping, quantification, differential expression analysis). But I don’t know how to choose a server. Could anyone can tell me to process such a dataset, how…

Name Last modified Size Description Parent Directory   –   duplication_levels.png 24-May-2014 17:58 17K   kmer_profiles.png 24-May-2014 17:58 433K   per_base_gc_content.png 24-May-2014 17:58 48K   per_base_n_content.png 24-May-2014 17:58 26K   per_base_quality.png 24-May-2014 17:58 32K   per_base_sequence_content.png 24-May-2014 17:58 96K   per_sequence_gc_content.png 24-May-2014 17:58 25K   per_sequence_quality.png 24-May-2014 17:58 19K  …

About ‘Estimated Number of cells’ in snRNA-seq 0 Hi all, I am analyzing single nucleus RNA-seq data using Seurat. And I have total four group and 24 samples (Brain region A Control & case and Brain region B Control & case; each n=6). I wonder what is the appropriate range…

We are currently searching for a Bioinformatics Scientist to provide support services to satisfy the overall operational objectives of the Center for Alzheimer’s and Related Dementias, National Institute on Aging. The primary objective is to provide services and deliverables through performance of support services. This opportunity is full-time, and it…

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…

Hi Lucas, got a weird one for you. If I change the caller from hapotypecaller to freebayes, I get the error below. It’s doubly strange because it seems to occur well before freebayes would be used in the pipeline. [Sat Dec 11 11:13:02 2021] rule samtools_stats: input: dedup/111D03-1.bam output: qc/samtools-stats/111D03-1.txt…

Dear @Mario_Garcia,The tool should work, I tested it right now with some test data. Please make sure: (a) your data was correctly analyzed by QualiMap BAM QC (i.e., the files should not be empty),(b) your files come from the same organism and data library(c) and you data has no weird…

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…

Hi! I played around with the Illumina mouse demo data and ENmix. The following code worked for me and you should end up with normalized beta values for subsequent limma analysis (or DMR analysis folowing the ENmix vignette). #setwd() #download the Infinium_Mouse_Methylation_v1.0_A1_GS_Manifest_File.csv file from Illumina HP to working directory (=…

Impact Healthcare Roche Sequencing is developing ground-breaking next-generation sequencing (NGS) products that allow scientists/clinicians powerful new avenues to investigate DNA, the blueprint of any lifeforms, in days enabling them to understand health conditions such as cancer, HIV, COVID19 and more! We are not only changing science but changing lives through…

As the Head of Services and Pharma Collaborations Bioinformatics, Molecular Lab Applications you will play a key role in growing Roche’s services business that supports key strategic initiatives in Oncology, Genetics, and Women’s Health. You will implement and manage bioinformatics operations for assays in Roche’s San Jose CLIA laboratory, and…

Company Description Addgene is a thriving nonprofit founded in 2004 that facilitates biomedical research and discovery. Our biorepository stores, archives, and distributes plasmids for scientists around the world. Addgene’s plasmid collection is used to advance research in a wide variety of disciplines, including cancer, heart disease, and neurodegenerative disorders, and…

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see flowTrans. Parameter Optimization for Flow Cytometry Data Transformation Bioconductor version: 2.9 Profile maximum likelihood estimation of parameters for flow cytometry data transformations. Author: Greg Finak <greg.finak at ircm.qc.ca>, Juan Manuel-Perez <jperez at ircm.qc.ca>,…

About Obsidian Therapeutics Obsidian Therapeutics is a biotechnology company using its proprietary cytoDRiVE™ technology to pioneer a new generation of controllable cell and gene therapies to treat diseases like cancer. Job Description About Us… Obsidian Therapeutics is pioneering engineered cell and gene therapies to deliver transformative outcomes for patients. Obsidian’s…

Now that you know nearly all the possibilities in this mod, let’s go even more deeper. Oct 15, 2019. Continue browsing in r/gmod. The original TF2 on the other hand is very easy to face pose, because you can literally move just 1 silder, and then you got a “happy…

Intensity of magnade’s attraction to a hunter. Learn how your comment data is processed. Find key bound to specified command string. Insomnia65 August 12, 2019 – TF2 Team. if you find this, don’t go around enabling it and then complaining about issues. The “size in K” is the block size…

What is the cutoff used for define high or low expression level of gene for survival analysis 1 Hi everyone In RNA-seq analysis, we need to separate samples into two groups for survival analysis. How can I define high level or low level for a gene according to counts or…

IMPUTE2 -merge_ref_panels 0 Hi all, i am trying to use IMPUTE2 with 2 reference panels to be merged. i am applying the code as per the example provided on IMPUTE2 page. but somehow the merged reference panel doesnt get produced (the REF file as per the example). any ideas? for…

About Us… Obsidian Therapeutics is pioneering engineered cell and gene therapies to deliver transformative outcomes for patients. Obsidian’s programs apply our CytoDriveTM technology in Cell and Gene therapy products to control expression of proteins for enhanced therapeutic efficacy and safety. We’re proud of our diverse talented team and committed to…

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

We are currently looking for a Bioinformatics Scientist to join a leading biotech company based in the Cambridge area. As the Bioinformatics Scientist you will drive the development of computational tools and perform omics data analysis to support target identification and therapeutics development platforms KEY DUTIES AND RESPONSIBILITIES: Your duties…

Generation of Illumina Microarray Quality control 0 Hi, I’m getting myself familiar with some microarray data analysis. I’m trying to follow the Infinium Controls training guide from illumina, but my working computer is not Windows (I’m using Linux), so is there any way that I can generate the QC report…

If you are a Senior Bioinformatics Scientist with experience, please read on! We are a Gene Therapy start up focused on using a holistic approach to bring manufacturing, engineering and research all under one roof.Top Reasons to Work with Us1. We have closed 10s of millions in funding 2. We…

Remove related samples using plink 0 Hi, I generated pairwise IBD (PI_HAT) using plink1.9 –genome option. I have >200,000 samples, so I used –parallel and combined the sub files using cat. Is there a way to remove related samples using the output file .genome.gz ? I read about –rel-cutoff but…

Explore LabKey Server’s specialized tools for assay data management below and read additional documentation on the LabKey support and documentation portal. Flow. Using SQL Search you can search for the column name and find all the stored procedures where it is used. Work faster. Finding anything in the Object Explorer….

Hi. I’m doing ATAC-seq analysis of colon tissue. I analyzed 1)QC -> 2)Mapping -> 3)Post alignment processing(remove mt reads, duplicated reads, multi-mapped reads) -> 4)Peak calling order. However, as a result of calculating FRiP after peak calling using MACS2, the FRiP score was too low. No major problems were found…

Edit June 7, 2020: The code below is for pre-phasing with SHAPEIT2. For phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs, see my answer here: A: ERROR: You must specify a valid interval for imputation using the -int argument, So, the steps are usually: pre-phasing…

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…

Manager, Bioinformatics Brain Science The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make…

validation of probable SNPs 0 Hi all, I recently got some significant SNPs from my GWAS analysis, many of these SNPs are imputed (I filtered Rsq>0.8 ). We are yet to do replication study for our findings, waiting for replication cohort samples and it might take a while for this….

Hello, I got a very weird output from BWA-mem2 – most of the reads have mapping quality of 0, even though there is no secondary alignment or anything else suspicious. I got sequencing data that was aligned with Novoalign to hg18, the data was bam files. I needed to realign…

Strategy and design of the method We sought to develop a simple method to increase the sequencing capability of PacBio CCS to sequence several diverse DNA libraries ~ 870 bp in length that encoded protein variants originating from a directed evolution campaign. To achieve an increase in the throughput of a PacBio sequencing…

What is the best QC to do on imputed UK Biobank data? 0 I am receiving imputed data from UK Biobank to conduct a GWAS on. Previously I have carried out GWAS on genotype data, which I have QC’d for missingness per individual and per SNP, sex discrepancy, MAF filter…

Dublin, Sept. 09, 2021 (GLOBE NEWSWIRE) — The “Global Next-Generation Sequencing Data Analysis Market Size, Share & Trends Analysis Report by Product, by Workflow, by Mode, by Read Length, by End-use, by Region, and Segment Forecasts, 2021-2028” report has been added to ResearchAndMarkets.com‘s offering. The global next-generation sequencing data analysis…

Dublin, Sept. 09, 2021 (GLOBE NEWSWIRE) — The “Global Next-Generation Sequencing Data Analysis Market Size, Share & Trends Analysis Report by Product, by Workflow, by Mode, by Read Length, by End-use, by Region, and Segment Forecasts, 2021-2028” report has been added to ResearchAndMarkets.com‘s offering. The global next-generation sequencing data analysis…

Position Description: Every great life-changing discovery begins the same way-with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do…

Position Description: Every great life-changing discovery begins the same way-with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do…

How to pass custom software specific variables to nf-core/sarek nextflow pipeline? 0 I’m attempting to call whole genome variants using nf-core/sarek nextflow pipeline. In QC step there is an option that invokes trim_galore quality trimming, but i don’t know how to pass my custom adapters to be cut as well….

Job DescriptionBioinformatics ScientistFull Time Direct Hire Remote positionAre you looking for bioinformatics work? Are you interested in joining a team of talented bioinformaticians dedicated to understanding the genetics of cancer? In this role you will:* Function as a scientific thought leader within for all aspects of GWAS and population genetics….

Commandline BLAST – errors? 0 Hi, I’m running command line blastx and blastp against a number of databases. However, running the exact same script on the exact same input files against the exact same databases occasionally seems to output different filesizes. I can only assume that this is because the…

It holds a 15% stake in the company and has valued its holding at £340m, giving a valuation of more than £2bn for the company. . While the company’s current shareholders have recorded its value at just over £2bn, analysts . Essay from the year 2011 in the subject Business…