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output data (files in.idat format)  (Illumina Inc)


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    Structured Review

    Illumina Inc output data (files in.idat format)
    Output Data (Files In.Idat Format), supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/format+data+files/sequencing+data+output/pm39847262-60-0-0
    Average 90 stars, based on 1 article reviews
    output data (files in.idat format) - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: Painful diabetic neuropathy is associated with accelerated epigenetic aging
    Article Snippet: Illumina output data (files in .idat format) from the experiments were parsed and preprocessed using minfi package within R software (version 3.6.3).

    Article Title: ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications.
    Article Snippet: Project home page: - GitHub https:// github. com/ ncher ric/ Iliad - Read the Docs https:// iliad. readt hedocs. io/ - Sylabs Cloud (Singularity) https:// cloud. sylabs. io/ libra ry/ ncher ric/ iliad/ igdp- conta iner - Dockerhub https:// hub. docker. com/ repos itory/ docker/ ncher ric/ iliad/ gener al Operating system(s): Linux, Windows, and/or MacOS Programming language: Snakemake, Python, and Bash Other requirements: Singularity 3.6.4 or higher, Conda 4.13.0 or higher License The MIT License Documentation Creative Commons license CC-BY SA 3.0 Any restrictions to use by non-academics: None GWAS Genome-wide association study SNP Single nucleotide polymorphism IAAP-CLI Illumina Array Analysis Platform Genotyping Command Line Interface CRAM Compressed Reference-oriented Alignment Map HGDP Human Genome Diversity Project GB Gigabyte SNV Single nucleotide variant SV Structural variant VCF Variant call format FTP File transfer protocol HPC High-performance computing NGS Next-generation sequencing rsID Reference SNP cluster identifier FASTA Sequence data file format FASTQ Extension of FASTA to include sequence quality data along with sequence data IDAT Intensity data IUPUI Indiana University-Purdue University Indianapolis BAM Binary alignment map SAM Sequence alignment map WGS Whole genome sequence BWA Burrows-Wheeler aligner IRB Institutional Review Board Supplementary Information The online version contains supplementary material available at https:// doi. org/ 10.

    Article Title: Painful diabetic neuropathy is associated with accelerated epigenetic aging.
    Article Snippet: Illumina output data (files in.idat format) from the experiments were parsed and preprocessed using minfi package within R software (version 3.6.3).

    Article Title: Prevalence of the cancer-associated germline variants in Russian adults and long-living individuals: using the ACMG recommendations and computational interpreters for pathogenicity assessment
    Article Snippet: FASTQ files were obtained by demultiplexing the sequencing data in BCL format using Illumina bcl2fastq2 v2.20.0.422 Conversion Software.

    Article Title: Draft genome sequence of two "Candidatus Intestinicoccus colisanans" strains isolated from faeces of healthy humans.
    Article Snippet: Analysis with dbCAN2 Data file 1 MH27-1 and MH27-2 NCBI BioProject No file format NCBI BioProject Database https://identifiers.org/ncbi/ bioproject:PRJNA7795 [13] Data file 2 MH27-1 Illumina raw sequences fastq NCBI Sequence Read Archive https://identifiers.org/ncbi/ insdc.sra:SRX13161736 [14] Data file 3 MH27-1 whole genome assembly sequence fasta NCBI Assembly Database https://identifiers.org/ncbi/assembly:GCA_021029585.1 [15] Data file 4 MH27-2 Illumina raw sequences fastq NCBI Sequence Read Archive https://identifiers.org/ncbi/ insdc.sra:SRX13161735 [16] Data file 5 MH27-2 whole genome assembly sequence fasta NCBI Assembly Database https://identifiers.org/ncbi/ assembly:GCA_021029595.1 [17] revealed MH27-1 and MH27-2 encode 44 and 45 carbohydrate active enzymes respectively, including four copies of GH5 (cellulase) and GH29 (fucosidase) enzymes each.

    Sequencing:

    Article Title: Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates
    Article Snippet: Libraries were then pooled evenly by molarity and sequenced on a shared Illumina NovaSeq6000 150PE S4 flowcell. .. Raw sequencing data was converted into fastq format sample specific files using the Illumina BCL Convert V4 software on the sequencing center’s local Linux server system. ..

    Article Title: A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer.
    Article Snippet: Libraries were pooled evenly by molarity and sequenced on an Illumina NovaSeq6000 150PE S4. .. Raw sequencing data were converted into fastq format, sample-specific files using the Illumina bcl2fastq2 software on the sequencing centers local Linux server system. ..

    Article Title: Small RNA signatures of the anterior cruciate ligament from patients with knee joint osteoarthritis
    Article Snippet: The pooled libraries were sequenced on an Illumina HiSeq 4000 platform with sequencing chemistry version 1 to generate 2 × 150 bp paired-end reads. .. Read files in FASTQ format were generated from sequence data measured from one lane of an Illumina HiSeq 4000 through basecalling and de-multiplexing of indexed reads using CASAVA version 1.8.2 and adapter and quality trimming using Cutadapt version 1.2.1 ( ) and Sickle version 1.200. .. Small RNA expression values were obtained through aligning reads to Ensembl GRCH38.96 human genome reference sequences using TopHat ( ) version 2.0.10 with the option “–g 1”, counting aligned reads against gene features using HTSeq-count version 0.6.1p1, and filtering genes by biotype and keeping the small RNA genes for further analysis.

    Software:

    Article Title: Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates
    Article Snippet: Libraries were then pooled evenly by molarity and sequenced on a shared Illumina NovaSeq6000 150PE S4 flowcell. .. Raw sequencing data was converted into fastq format sample specific files using the Illumina BCL Convert V4 software on the sequencing center’s local Linux server system. ..

    Article Title: A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer.
    Article Snippet: Libraries were pooled evenly by molarity and sequenced on an Illumina NovaSeq6000 150PE S4. .. Raw sequencing data were converted into fastq format, sample-specific files using the Illumina bcl2fastq2 software on the sequencing centers local Linux server system. ..

    Generated:

    Article Title: Small RNA signatures of the anterior cruciate ligament from patients with knee joint osteoarthritis
    Article Snippet: The pooled libraries were sequenced on an Illumina HiSeq 4000 platform with sequencing chemistry version 1 to generate 2 × 150 bp paired-end reads. .. Read files in FASTQ format were generated from sequence data measured from one lane of an Illumina HiSeq 4000 through basecalling and de-multiplexing of indexed reads using CASAVA version 1.8.2 and adapter and quality trimming using Cutadapt version 1.2.1 ( ) and Sickle version 1.200. .. Small RNA expression values were obtained through aligning reads to Ensembl GRCH38.96 human genome reference sequences using TopHat ( ) version 2.0.10 with the option “–g 1”, counting aligned reads against gene features using HTSeq-count version 0.6.1p1, and filtering genes by biotype and keeping the small RNA genes for further analysis.



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