Tag: QC

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…

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>,…

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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…

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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…

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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…

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…

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…

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…

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…

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…

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…

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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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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,…

© 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…

genomic inflation factor (lambda)=1 0 Dear Community members, Does genomic inflation (lambda)= 1 indicate that there is no obvious population stratification in GWAS? I did GWAS (binary phenotype) and while running –glm in plink2, the output gives lambda=1. Even when i don’t include my principal components the lambda value is…

How to fix phenotype information when converting from VCF to PLINK 0 I have a series of VCF files (one for each chromosome) that have an incorrect values for the phenotype (all samples have the value “-9”). I have read on other questions that the make-pheno or pheno flags can…

Bismark rrbs data analysis 1 Hello! I’m quite new in methyl-seq data. And I’ve just completed a RRBS analysis on bismark. So I got some text file results but I’m not quite sure how to interpret these data. What is the best tool to make them visual? Some of the…

How to properly combine two bam files of a paired-end data 3 Hi all! I am mapping a paired-end read separately using bowtie2. After that, I want to combine the two bam file into one for downstream analysis. How to properly do this combination? I tried: samtools sort -n R1.bam…

I struggle to infer relationships in a dataset of 20K exomes from tens of kits. At first I found a well-covered union of regions – check. Second, I performed everything to merge 20K VCFs into one. Removed indels and multi-allelic variants. Check. Still, when I run KING with “kinship” option,…

This is a very difficult question to answer precisely. The theoretical argument is clear (based on information content literature), but in practice there are a lot of ways to muddy the waters…Let me give a theoretical argument first, then make several practical arguments afterwards. I hope that will do an…

Integrated Dimension Reduction Plot for CD4/CD8 sorted Feedback 1 Hello, I have recently followed adopted the Harvard Chan Bioinformatics Core guidelines for SC QC/Normalization/Clustering (hbctraining.github.io/scRNA-seq_online/schedule/links-to-lessons.html). I have integrated CD4+/CD8+ T cells from two time points. I recently received feedback that my integrated dimension reduction plot clustering looked problematic. Specifically, the…