Tag: QC

Reporting results from fastp Read GC content

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…

Continue Reading Reporting results from fastp Read GC content

Frontiers | Serum and Serum Exosomal CircRNAs hsa_circ_0001492, hsa_circ_0001439, and hsa_circ_0000896 as Diagnostic Biomarkers for Lung Adenocarcinoma

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…

Continue Reading Frontiers | Serum and Serum Exosomal CircRNAs hsa_circ_0001492, hsa_circ_0001439, and hsa_circ_0000896 as Diagnostic Biomarkers for Lung Adenocarcinoma

cfDNA-Based NGS IG Analysis in Lymphoma

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,…

Continue Reading cfDNA-Based NGS IG Analysis in Lymphoma

Singular Genomics Partners with Qiagen to Enable Qiaseq Kits for the G4 Sequencing Platform

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…

Continue Reading Singular Genomics Partners with Qiagen to Enable Qiaseq Kits for the G4 Sequencing Platform

Read counts an order of magnitude higher on one chromosome

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…

Continue Reading Read counts an order of magnitude higher on one chromosome

Bispecific antibodies | Scientist Live

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…

Continue Reading Bispecific antibodies | Scientist Live

Get reference genome from Kraken2 taxID

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…

Continue Reading Get reference genome from Kraken2 taxID

Help me understand the Nanopore fastqc results

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…

Continue Reading Help me understand the Nanopore fastqc results

Strange Per base sequence content of fastqc

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…

Continue Reading Strange Per base sequence content of fastqc

Bioinformatics Data Engineer in Boston, MA for Dana-Farber Cancer Institute

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…

Continue Reading Bioinformatics Data Engineer in Boston, MA for Dana-Farber Cancer Institute

Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing

** 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…

Continue Reading Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing

Manager of Bioinformatics in Chicago, IL for University of Chicago (UC)

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,…

Continue Reading Manager of Bioinformatics in Chicago, IL for University of Chicago (UC)

Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

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…

Continue Reading Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Genomic Analysis Reveals a New Dominant Lineage of SARS-CoV-2

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…

Continue Reading Genomic Analysis Reveals a New Dominant Lineage of SARS-CoV-2

different result using minimap2 and pbmm2

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…

Continue Reading different result using minimap2 and pbmm2

Conducting Respiratory Oscillometry in an Outpatient Setting

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…

Continue Reading Conducting Respiratory Oscillometry in an Outpatient Setting

pjotrp/sambamba – sambamba – Genenetwork

10 years ago ​ 10 years ago ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10 years ago ​ ​ ​ ​ ​ ​ 10 years ago 10 years ago 10 years ago ​ ​ 10 years ago ​ 10 years…

Continue Reading pjotrp/sambamba – sambamba – Genenetwork

Mapping back 3 sets of reads/sample with minimap2

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,…

Continue Reading Mapping back 3 sets of reads/sample with minimap2

dx: error: unrecognized arguments: running swiss army knife plink2

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…

Continue Reading dx: error: unrecognized arguments: running swiss army knife plink2

I wonder if someone please explain what secondary, supplementary, duplicates and paired in sequencing mean in samtools flagstat

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 +…

Continue Reading I wonder if someone please explain what secondary, supplementary, duplicates and paired in sequencing mean in samtools flagstat

Interactive Shiny App for Bulk Sequencing Data

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…

Continue Reading Interactive Shiny App for Bulk Sequencing Data

HRJOB7442 Bioinformatics Scientist 2 (Various Locations) in Nether Alderley, Macclesfield (SK10) | Almac Group (Uk) Ltd

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…

Continue Reading HRJOB7442 Bioinformatics Scientist 2 (Various Locations) in Nether Alderley, Macclesfield (SK10) | Almac Group (Uk) Ltd

Extracellular circulating miRNAs as stress-related signature to search and rescue dogs

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…

Continue Reading Extracellular circulating miRNAs as stress-related signature to search and rescue dogs

Additonal file 4

%PDF-1.5 % 1 0 obj >/OCGs[30 0 R]>>/Type/Catalog>> endobj 71 0 obj >stream application/pdf Additonal file 4 Adobe Illustrator CS3 2012-03-05T13:34:16-06:00 2012-03-05T13:34:16-06:00 2012-03-05T13:34:16-06:00 196 256 JPEG /9j/4AAQSkZJRgABAgEASABIAAD/7QAsUGhvdG9zaG9wIDMuMAA4QklNA+0AAAAAABAASAAAAAEA AQBIAAAAAQAB/+4ADkFkb2JlAGTAAAAAAf/bAIQABgQEBAUEBgUFBgkGBQYJCwgGBggLDAoKCwoK DBAMDAwMDAwQDA4PEA8ODBMTFBQTExwbGxscHx8fHx8fHx8fHwEHBwcNDA0YEBAYGhURFRofHx8f Hx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8fHx8f/8AAEQgBAADEAwER AAIRAQMRAf/EAaIAAAAHAQEBAQEAAAAAAAAAAAQFAwIGAQAHCAkKCwEAAgIDAQEBAQEAAAAAAAAA AQACAwQFBgcICQoLEAACAQMDAgQCBgcDBAIGAnMBAgMRBAAFIRIxQVEGE2EicYEUMpGhBxWxQiPB UtHhMxZi8CRygvElQzRTkqKyY3PCNUQnk6OzNhdUZHTD0uIIJoMJChgZhJRFRqS0VtNVKBry4/PE 1OT0ZXWFlaW1xdXl9WZ2hpamtsbW5vY3R1dnd4eXp7fH1+f3OEhYaHiImKi4yNjo+Ck5SVlpeYmZ qbnJ2en5KjpKWmp6ipqqusra6voRAAICAQIDBQUEBQYECAMDbQEAAhEDBCESMUEFURNhIgZxgZEy obHwFMHR4SNCFVJicvEzJDRDghaSUyWiY7LCB3PSNeJEgxdUkwgJChgZJjZFGidkdFU38qOzwygp 0+PzhJSktMTU5PRldYWVpbXF1eX1RlZmdoaWprbG1ub2R1dnd4eXp7fH1+f3OEhYaHiImKi4yNjo +DlJWWl5iZmpucnZ6fkqOkpaanqKmqq6ytrq+v/aAAwDAQACEQMRAD8A6k3/ADkv+XCO8c31qB4z xkWX6rHxapHElrgCtQfuOKqyf85F+Q5IfrCQXzW3MR/WAlv6XJl5gF/X4iq71Jpiqin/ADkv+W7i sZuZBQmqfVWHwqXO4nP7Kk4qqxf85G/l/LzEaXbMkUk7JS25hIk9ST4PX5VVRUrSvtirJfLf5iQ+ ZdKTVdF0TUbqwlJEc1bKOtKH7Ml0jd+4xVMLnV9Tnt5YG8u6kqyoyFhJp1QGFKit3irwvTLvyFov mKTSIfMvmaLUopljuLA6hYoSbAKJIndJ0JASApTl3IG9KKqC+e/y/toXhm88ea3d9hcyalbgrziM a0K3Cx7MpcVHXrirM/J99p3mvyvq+nafda75gguJojc3xubUtFST6xEsXrXj8OUfENwoO4C9AqiU /LWI2iWtxp2uXEUcUsCcn0lWCTTwTt8aXCvWtuVBrsrtTDasN81az5W0PW7vSdQ80+bfL1yLi6vP qEF1ZQwRrccLlo4ykpTggnBUcq7mnQ4FSfUPPvlAWs0Vt+YPma3lnjIjubm6ikdWkkRlkRY7y3Tj w5LsvcMCvE1VZ15b0Ma9o1w9jqXm7WNLuYDbMbq8sXUma3jPOktwpJ4uHHgxxViMf5g/lU1h/h+D zH5gtUklmnZYprS1Di4MIMLMksQKqsPFUJ5BXP8Ak0VehXXlfUIIIrET+bLRr26Is/q97p8aoRAX MKKlzxVOMDPv3r3OKsRl85+T9G8xOb7zZ5oM1rIILrTpL+1eFZLJ0jlV+NweBZ4GD/FvyPjiqe2/ lm11Gw0qxM/mjVProXWbK8urvT7h5YbdWTmrvccVWmoxkDxCmmxxVjllq3kjz3PZeX9E17zLJMmn RwxabDcWUKSRRR/3/oySonqcdyQK+PairLbb89/I3lmIaBqcuqTX+nyyWlxLfm2kuGlSXg3NxPRq M1OXSmKou1/5yR/Lu5mggj+sia5l9CKOQ2sTGXkE4kSXC8TyYD4qYqnGv/nFoPl7SrDVta06/stP 1IKbKd/qZD8k9QbJcsVqv81PDriqRf8AQzX5aUZi1yqqqOXb6qF4yAMtGM9CaMKgbjviqoP+ck/y 5M3og3Jk/d8Vra/F6qB04f6R8Xwnfj06HfFUZ5f/AD88meYdWi0jRoLu71KYkRWqm0RmIiaY053C j+7Rm+jFWX/4m/cV/Rt39c+s/VP0fW29b1PR+sfa9b0ael8X957dcVfJPn+9vNP07y4NEisrf1rQ veHT1XU3dlSOhn9WJfRb4jRVr3qds0eiJlKfGZ7S2v09/Kju3z2Ap6FpdrojXbC4stBkb6jZly+q…

Continue Reading Additonal file 4

Notch activation suppresses endothelial cell migration and sprouting via miR-223-3p targeting Fbxw7

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 …

Continue Reading Notch activation suppresses endothelial cell migration and sprouting via miR-223-3p targeting Fbxw7

Comprehensive circRNA Analyses in Human Vertebrae of GIOP and Its Molecular Mechanism

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…

Continue Reading Comprehensive circRNA Analyses in Human Vertebrae of GIOP and Its Molecular Mechanism

Combining multiple 10x scRNAseq datasets

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…

Continue Reading Combining multiple 10x scRNAseq datasets

Introduction to RNA-seq data analysis – Extended Materials

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…

Continue Reading Introduction to RNA-seq data analysis – Extended Materials

Samtools flagstat confusing result of a merged bam file

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…

Continue Reading Samtools flagstat confusing result of a merged bam file

[SOLVED] changing the order of input changes samtools merge ouput

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…

Continue Reading [SOLVED] changing the order of input changes samtools merge ouput

Plink Alternative Phenotype File Columns not being Read

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…

Continue Reading Plink Alternative Phenotype File Columns not being Read

Bioconductor – RiboCrypt

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….

Continue Reading Bioconductor – RiboCrypt

The Genetic Architecture of Sleep Health Scores in the UK

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…

Continue Reading The Genetic Architecture of Sleep Health Scores in the UK

python – Missing input files after defining them in function

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…

Continue Reading python – Missing input files after defining them in function

Overestimation of number of reads from nanopore data (flagstat)

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% :…

Continue Reading Overestimation of number of reads from nanopore data (flagstat)

Samtools flagstat

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…

Continue Reading Samtools flagstat

Associate Director, Bioinformatics Job Opening in Wilmington, DE at Incyte Corporation

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…

Continue Reading Associate Director, Bioinformatics Job Opening in Wilmington, DE at Incyte Corporation

Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

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 …

Continue Reading Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

RNA-seq analysis cloud server

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…

Continue Reading RNA-seq analysis cloud server

Index of /readarchive/Miseq/2014_05_21_run_miseq/Adapter_trimmed_nextera_samples/QC_after_trimming/Geo33_S19.R1.trimmed.paired_fastqc/Images

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  …

Continue Reading Index of /readarchive/Miseq/2014_05_21_run_miseq/Adapter_trimmed_nextera_samples/QC_after_trimming/Geo33_S19.R1.trimmed.paired_fastqc/Images

About ‘Estimated Number of cells’ in snRNA-seq

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…

Continue Reading About ‘Estimated Number of cells’ in snRNA-seq

BioSpace hiring Bioinformatics Scientist in Bethesda, Maryland, United States

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…

Continue Reading BioSpace hiring Bioinformatics Scientist in Bethesda, Maryland, United States

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…

Continue Reading Benchmarking the NVIDIA Clara Parabricks germline pipeline on AWS

[moiexpositoalonsolab/grenepipe] freebayes causes early error about number of threads

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…

Continue Reading [moiexpositoalonsolab/grenepipe] freebayes causes early error about number of threads

QualiMap Multi-Sample BamQC does not load in center panel – usegalaxy.eu support

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…

Continue Reading QualiMap Multi-Sample BamQC does not load in center panel – usegalaxy.eu support

Nanopore metagenomics: from sample to analysis

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…

Continue Reading Nanopore metagenomics: from sample to analysis

How to analyze Infinium Mouse Methylation BeadChip array data?

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 (=…

Continue Reading How to analyze Infinium Mouse Methylation BeadChip array data?

Roche hiring Principal Bioinformatics Scientist I in Santa Clara, California, United States

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…

Continue Reading Roche hiring Principal Bioinformatics Scientist I in Santa Clara, California, United States

Roche hiring Head of Pharma Services Bioinformatics, Molecular Lab Applications in Pleasanton, California, United States

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…

Continue Reading Roche hiring Head of Pharma Services Bioinformatics, Molecular Lab Applications in Pleasanton, California, United States

Co-op DNA Sequencing QC/QA – Addgene

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…

Continue Reading Co-op DNA Sequencing QC/QA – Addgene

Bioconductor – flowTrans

    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>,…

Continue Reading Bioconductor – flowTrans

Obsidian Therapeutics hiring Associate Director, Computational Biology/Bioinformatics in Cambridge, MA, US

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…

Continue Reading Obsidian Therapeutics hiring Associate Director, Computational Biology/Bioinformatics in Cambridge, MA, US

gmod how to animate ragdolls

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…

Continue Reading gmod how to animate ragdolls

gmod animation commands

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…

Continue Reading gmod animation commands

What is the cutoff used for define high or low expression level of gene for survival analysis

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…

Continue Reading What is the cutoff used for define high or low expression level of gene for survival analysis

IMPUTE2 -merge_ref_panels

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…

Continue Reading IMPUTE2 -merge_ref_panels

Associate Director, Computational Biology/Bioinformatics Job Opening in Cambridge, MA at Obsidian Therapeutics

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…

Continue Reading Associate Director, Computational Biology/Bioinformatics Job Opening in Cambridge, MA at Obsidian Therapeutics

Question about ROH analysis by Plink 1.9

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…

Continue Reading Question about ROH analysis by Plink 1.9

Bioinformatics Scientist – reed.co.uk

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…

Continue Reading Bioinformatics Scientist – reed.co.uk

Generation of Illumina Microarray Quality control

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…

Continue Reading Generation of Illumina Microarray Quality control

CyberCoders hiring Senior Bioinformatics Scientist in Boston, Massachusetts, United States

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…

Continue Reading CyberCoders hiring Senior Bioinformatics Scientist in Boston, Massachusetts, United States

Remove related samples using plink

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…

Continue Reading Remove related samples using plink

Sql Server Import From Excel With Sql, Duplicate Column Names

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….

Continue Reading Sql Server Import From Excel With Sql, Duplicate Column Names

low FRiP(Fraction of Reads in Peaks) score in ATAC-seq

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…

Continue Reading low FRiP(Fraction of Reads in Peaks) score in ATAC-seq

Phasing with SHAPEIT

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…

Continue Reading Phasing with SHAPEIT

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…

Continue Reading Picard CalculateHsMetrics perTargetCoverage for Novaseq bams

Manager, Bioinformatics – Brain Science job in Seattle, WA | Allen Institute for Brain Science

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…

Continue Reading Manager, Bioinformatics – Brain Science job in Seattle, WA | Allen Institute for Brain Science

validation of probable SNPs

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….

Continue Reading validation of probable SNPs

MAPQ (Mapping quality) of 0 for most reads from BWA-MEM2 (with no secondary alignment or other apparent reason)

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…

Continue Reading MAPQ (Mapping quality) of 0 for most reads from BWA-MEM2 (with no secondary alignment or other apparent reason)

PacBio sequencing output increased through uniform and directional fivefold concatenation

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…

Continue Reading PacBio sequencing output increased through uniform and directional fivefold concatenation

What is the best QC to do on imputed UK Biobank data?

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…

Continue Reading What is the best QC to do on imputed UK Biobank data?

Worldwide Next-Generation Sequencing Data Analysis Industry to 2028

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…

Continue Reading Worldwide Next-Generation Sequencing Data Analysis Industry to 2028

Worldwide Next-Generation Sequencing Data Analysis Industry

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…

Continue Reading Worldwide Next-Generation Sequencing Data Analysis Industry

Bioinformatics Analyst I – Job at Medical College of Wisconsin in Milwaukee, WI

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…

Continue Reading Bioinformatics Analyst I – Job at Medical College of Wisconsin in Milwaukee, WI

Bioinformatics Analyst II – Job at Medical College of Wisconsin in Menomonee Falls, WI

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…

Continue Reading Bioinformatics Analyst II – Job at Medical College of Wisconsin in Menomonee Falls, WI

How to pass custom software specific variables to nf-core/sarek nextflow pipeline?

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….

Continue Reading How to pass custom software specific variables to nf-core/sarek nextflow pipeline?

Bioinformatics Scientist in Frederick, MD

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….

Continue Reading Bioinformatics Scientist in Frederick, MD

Commandline BLAST – errors?

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…

Continue Reading Commandline BLAST – errors?

nanopore sequencing stock

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…

Continue Reading nanopore sequencing stock

Research Scientist Bioinformatics at Exscientia

We are looking to hire an experienced bioinformatician who specializes in the analysis of human NGS data. The Research Scientist Bioinformatics will lead the development and expansion of our in-house NGS capabilities together with data managers and software developers, while also carrying out project-specific analyses. Exscientia GmbH is a company…

Continue Reading Research Scientist Bioinformatics at Exscientia

Senior Bioinformatician / Developer (Analysis Pipelines) at Earlham Institute

Applications are invited for a Senior Bioinformatician / Developer to join the Laboratory of Dr David Swarbreck in the Digital Biology Programme at the Earlham Institute, based in Norwich, UK. Background: The Core Bioinformatics Group employ cutting edge technologies and computational approaches to deliver high-quality data analysis and develop software…

Continue Reading Senior Bioinformatician / Developer (Analysis Pipelines) at Earlham Institute

Should you remove reads below certain length ?

Nanopore: Should you remove reads below certain length ? 0 Hi there, We are using Nanopore for some transcriptomics analysis and I am building a QC pipeline. There is a default statement that it could be good to remove reads below 500 bp in length but I could not find…

Continue Reading Should you remove reads below certain length ?

Job vacancy in Global Worldwide: Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

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…

Continue Reading Job vacancy in Global Worldwide: Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

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…

Continue Reading Interpreting read coverage over gene body plot

Gene mutation analysis in papillary thyroid carcinoma

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

Continue Reading Gene mutation analysis in papillary thyroid carcinoma

Twist Bioscience hiring Bioinformatics Scientist, Production Bioinformatics in South San Francisco, California, United States

Twist is looking for a Bioinformatics Scientist to join our Production Bioinformatics Team. You will work alongside research scientists, software engineers and data scientists to further deliver on our mission to expand access to best-in-class synthetic biology and next-generation sequencing applications. You will be developing and engineering tools to better…

Continue Reading Twist Bioscience hiring Bioinformatics Scientist, Production Bioinformatics in South San Francisco, California, United States

Performing population stratification based on GWA tutorial

Performing population stratification based on GWA tutorial 0 Hi, I’m performing QC steps of Andries T. Marees GWA tutorial, currently I’m stuck at 7th step where you should begin the population stratification downloading a 61GB vcf.gz file of 1000genomes containing genetic data of 629 individuals from different ethnic backgrounds. Successively…

Continue Reading Performing population stratification based on GWA tutorial

Bioinformatics Analyst I – Genomic Analysis Laboratory, Dr. Joseph Ecker in San Diego, CA, 92101, USA

Job Details Description Application Instructions: Employment History Include your last ten (10) years of employment history, or length of your employment history if less, including all positions (even those that are not relevant to this position) and periods of unemployment. Incomplete information could disqualify you from further consideration. POSITION SUMMARY…

Continue Reading Bioinformatics Analyst I – Genomic Analysis Laboratory, Dr. Joseph Ecker in San Diego, CA, 92101, USA

Differential Gene Expression

Can you analyze in GEO2R? => No, because this is RNA-seq and not microarrays. You are lucky thought that the authors seem to provide raw counts so you can easily fede them into DESeq2. Here is a code suggestion, for details please read the DESeq2 vignette extensively, it contains answers…

Continue Reading Differential Gene Expression

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

This article was originally published here PLoS Comput Biol. 2021 Aug 24;17(8):e1009290. doi: 10.1371/journal.pcbi.1009290. Online ahead of print. ABSTRACT Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells…

Continue Reading miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

Output per variant and per sample heterozygosity fraction from VCF.

Output per variant and per sample heterozygosity fraction from VCF. 2 As a QC measure I would like to know the per variant and per sample heterozygosity fraction. I already used vcftools to output the missingness per variant and sample. vcftools.github.io/man_latest.html Is there any tool that can do the same…

Continue Reading Output per variant and per sample heterozygosity fraction from VCF.

Roche hiring Head of Reagents Bioinformatics, Molecular Lab Applications in Pleasanton, California, United States

As the Head of Reagent Bioinformatics in the Molecular Lab Applications chapter you will play a key role in advancing Roche’s class leading portfolio of sequencing reagents across sample preparation, library preparation, and target enrichment. Working in close partnership with wet lab, software, and commercial colleagues, you will build a…

Continue Reading Roche hiring Head of Reagents Bioinformatics, Molecular Lab Applications in Pleasanton, California, United States

Filter duplicate ID from PLINK file

Filter duplicate ID from PLINK file 0 Hi All, I am new to SNP-chip data analysis. I have been exploring some SNP-chip data using plink 1.9, while checking the Relatedness using KING, I am getting an error of duplicate ID. I was wondering if there is any method I can…

Continue Reading Filter duplicate ID from PLINK file

removing adaptor

removing adaptor 1 I have two RNAseq datasets, from two different sequencing core facilities – the fastq files they provide already are demultiplexed and trimmed for adaptor. This is the Adaptor content following fastqc-> multiqc . According to the multiqc all files passed the qc for adapter content. So I…

Continue Reading removing adaptor

Download bigWig files of publicly available ChIP-seq samples

Download bigWig files of publicly available ChIP-seq samples 1 There are a couple of efforts to provide quality controls of publicly available ChIP-seq data sets (e.g. www.ngs-qc.org/ and CISTROME. But is there a way to obtain the normalized bigWig files? Cistrome, for example, allows you to explore the coverage data…

Continue Reading Download bigWig files of publicly available ChIP-seq samples

very low coverage when mappin genomic DNA

very low coverage when mappin genomic DNA 0 Hi all, I’m having terrible problems to map/align single end RNA files from human genome (GRCh.38). It is genomic DNA but was prepared by using a RNA library kit to preserve strand specificity. I’ve first tried STAR and Kallisto and the coverage…

Continue Reading very low coverage when mappin genomic DNA

How filter genes to construct co-expression network?

How filter genes to construct co-expression network? 1 Hi, I am interested to filter data for constructing co-expression network , Which parameter can i use to filter genes? As i know in WGCNA tutorial, it suggests not to use differential expressed genes(DEG) to filter genes. WGCNA Co-expreesion network DEG Filtering…

Continue Reading How filter genes to construct co-expression network?

linux for genomics

linux for genomics 0 hi everyone, I have just started learning genomics as a part of my bioinformatics degree and I’ve been introduced to linux for handling fastq files and using fast qc. can anybody suggest some good learning resources which is more inclined towards linux for genomics. bioinformatics linux…

Continue Reading linux for genomics

How to sub-sample .bam file to target coverage?

How to sub-sample .bam file to target coverage? 0 Hi, I have .bam files for blood samples from which I extract signals. Let’s assume my samples have a 30x coverage and my signal of interest is nicely detectable. To see how well the signal is detectable with lower coverage samples,…

Continue Reading How to sub-sample .bam file to target coverage?

Controlling Banana Xanthomonas Wilt Disease in East Africa

© Olena Danileiko Experts Leena Tripathi, Jaindra Nath Tripathi and Richard Goodman, provide a compelling analysis of controlling Banana Xanthomonas Wilt Disease in East Africa By way of an introduction, banana (Musa spp.) is one of the most common fruits worldwide. However, it is an important staple crop in the…

Continue Reading Controlling Banana Xanthomonas Wilt Disease in East Africa