Tag: GenomeStudio

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…

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,…

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,…

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…

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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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…

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 \…

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…

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…

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…

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…

    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…