Tag: GenomeStudio

ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications | BMC Bioinformatics

Pipeline architecture and configuration file Genomic data processing poses a challenge for genetic research studies because it involves multiple program dependency installations, vast numbers of samples with raw data from various next-generation sequencing (NGS) platforms, and inconsistent genetic variant ID and/or positions among datasets. The Iliad suite of genomic data…

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Idat raw data conversion

Idat raw data conversion 0 Hello everybody We have just started genotyping with GSA and generated first idat files. To QC we were advices to use GenomeStudio and for that we downloaded all the necessary files: bpm, egt, imap files from illumina website. Yet when we performed analysis in Genomestudio,…

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Sentrix Array Genotyping

Sentrix Array Genotyping 0 Hi all, I am currently trying to figure out how to work with genotyping data generated by a Sentrix array. The data I have is an output file from the Illumina GenomeStudio Software, namely a SampleName_FinalReport.txt file which contains the columns Sample ID , Sample Name,…

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Dissecting human population variation in single-cell responses to SARS-CoV-2

Sample collection The individuals of self-reported African (AFB) and European (EUB) descent studied are part of the EVOIMMUNOPOP cohort18. In brief, 390 healthy male donors (188 AFB and 202 EUB) were recruited between 2012 and 2013 in Ghent (Belgium), thus, before the COVID-19 pandemic. Blood was obtained from the healthy…

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Adipogenic and SWAT cells separate from a common progenitor in human brown and white adipose depots

Human samples Human adipogenic progenitor cells were isolated from the stromal vascular fraction of adipose tissue samples on the day they were obtained (surgery or biopsy) from four regions: (1) visceral adipose tissue (obtained during gallbladder surgery); (2) perirenal adipose tissue (obtained during nephrectomy surgery); (3) abdominal subcutaneous adipose tissue…

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Specialty Genomics Bioinformatics Scientist I (Production) Job Opening in Indianapolis, IN at Labcorp Drug Development – USA

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

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SNP concordance between NGS and SNParray

SNP concordance between NGS and SNParray 0 Hi, I have a sample ran with Illumina SNParray and WES, and I need to compare their data. What is the best method to compare them? I was trying using the VCF: From WES data I created a VCF, but from SNParray data…

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Manifest Reference Strand

Manifest Reference Strand 0 Hi I am trying to generate a vcf from SNP array data (genomestudio). So far I can convert to plink format from genomestudio and create a vcf via plink2 commands: plink2 \ –pedmap gs-out-plink \ –make-pgen \ –sort-vars \ –merge-x \ –out test-1 then: plink2 \…

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Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degenerations

Patients recruitment and interviews We included a total of 90 patients from 38 Sudanese families in this study with the following inclusion criteria: 1. Patients presenting with symptoms, signs, and/or history suggestive of SCD. 2. Non-genetic causes that can mimic neurological illnesses that resemble SCD due to pregnancy- or birth-related…

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Resources to learn illumina’s GenomeStudio?

Resources to learn illumina’s GenomeStudio? 1 Hi All, I need to process a SNP genotype data from illumina’s raw IDAT file, I have done some research and it seem that the first layer of processing require analysis through GenomeStudio.. But how can I begin to learn how to use GenomeStudio…

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Bioconductor – lumi

DOI: 10.18129/B9.bioc.lumi     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see lumi. BeadArray Specific Methods for Illumina Methylation and Expression Microarrays Bioconductor version: 3.12 The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina…

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The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines | Clinical Epigenetics

Methylation analysis pipelines The ENmix pipeline performs data preprocessing in a stepwise way, including ENmix background correction [1], RELIC dye bias correction [3], optional inter-array normalization, RCP probe-type bias correction [2], quality control, filtering of low-quality data points, and imputation. ENmix background correction employs a mixture of exponential and truncated…

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ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

    Significance To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth…

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