Colombo Anthony R, J Triche Timothy, Ramsingh Giridharan
Jane Anne Nohl Division of Division of Hematology and Center for the Study of Blood Diseases, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90033, USA.
F1000Res. 2017 Apr 27;6:586. doi: 10.12688/f1000research.11355.2. eCollection 2017.
The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments. We offer cloud-scale RNAseq pipelines , and available within Illumina's BaseSpace cloud application platform which expedites Kallisto preparatory routines, reliably calculates differential expression, and performs gene-set enrichment of REACTOME pathways Due to inherit inefficiencies of scale, Illumina's BaseSpace computing platform offers a massively parallel distributive environment improving data management services and data importing. deploys Kallisto for parallel cloud computations and is conveniently integrated downstream from the BaseSpace Sequence Read Archive (SRA) import/conversion application titled . annotates the Kallisto results by extracting structured information directly from source FASTA files with per-contig metadata, calculates the differential expression and gene-set enrichment analysis on both coding genes and transcripts. The cloud pipeline supports ENSEMBL transcriptomes and can be used downstream from the facilitating raw sequencing importing, SRA FASTQ conversion, RNA quantification and analysis steps.
最近推出的Kallisto伪比对器已从根本上简化了RNA测序实验中转录本的定量分析。我们提供云规模的RNAseq流程，可在Illumina的BaseSpace云应用平台中使用，该平台加快了Kallisto的准备程序，可靠地计算差异表达，并对REACTOME通路进行基因集富集分析。由于规模上固有的低效率，Illumina的BaseSpace计算平台提供了大规模并行分布式环境，改善了数据管理服务和数据导入。部署Kallisto进行并行云计算，并方便地集成到名为BaseSpace序列读取存档（SRA）导入/转换应用程序的下游。通过直接从带有每个重叠群元数据的源FASTA文件中提取结构化信息来注释Kallisto结果，对编码基因和转录本进行差异表达计算和基因集富集分析。该云流程支持ENSEMBL转录组，可在促进原始测序导入、SRA FASTQ转换、RNA定量和分析步骤的下游使用。
