Example provenance示例溯源
Yeast SNF2 example data sources
Yeast SNF2 示例数据来源
The reference and de novo example reports use the same public yeast WT versus snf2 knockout RNA-seq project. TAFFISH does not host the full raw sequencing archive on this site; the example data are prepared by the maintainer data app rnaseq-yeast-get-data, which records source URLs, checksums, accessions, fallback downloads, commands and manifests.
有参和无参示例报告使用同一个公开 yeast WT vs snf2 knockout RNA-seq 项目。TAFFISH 不在本站托管完整原始测序归档；示例数据由维护者数据 app rnaseq-yeast-get-data 准备，并记录来源 URL、checksum、accession、fallback 下载、命令和 manifest。
This page is a public reader summary. The canonical preparation details live in the data-preparation repository and in the provenance files shipped with each generated output tree.
本页是面向公开读者的摘要。权威准备细节以 数据准备仓库 以及每个生成输出目录中的溯源文件为准。
Primary source resources
主要来源资源
| Component组成部分 | Role in the examples在示例中的作用 | Source and identifier来源和标识 | Attribution note引用与归属说明 |
|---|---|---|---|
| Raw RNA-seq reads原始 RNA-seq reads | FASTQ input for the reference and de novo demonstration routes.有参和无参演示路线的 FASTQ 输入。 | ENA PRJEB5348 / NCBI BioProject PRJEB5348 | Cite accession PRJEB5348 and Gierlinski et al. 2015, DOI 10.1093/bioinformatics/btv425.引用 accession PRJEB5348 和 Gierlinski et al. 2015，DOI 10.1093/bioinformatics/btv425。 |
| Author metadata and counts作者元数据和计数 | Sample mapping, excluded replicate list and author-derived WT/Snf2 count matrix.样本映射、排除重复列表和作者派生 WT/Snf2 count matrix。 | bartongroup/profDGE48, commit 375dc0d57d9d1fa96a4245a6530e0fda34305891 |
Cite the upstream repository/commit together with the associated yeast RNA-seq study; check the repository for current reuse notes.同时引用上游仓库/commit 和对应 yeast RNA-seq 研究；再次分发前检查该仓库当前复用说明。 |
| Reference genome and annotation参考基因组和注释 | Reference-mode genome FASTA, feature-only GFF3, transcript extraction and index preparation.有参模式的 genome FASTA、feature-only GFF3、转录本提取和索引构建。 | Saccharomyces Genome Database, S288C R64.4.1 |
Attribute SGD / yeastgenome.org and follow the current SGD license and citation guidance.归属 SGD / yeastgenome.org，并遵循 SGD 当前许可和引用说明。 |
| Gene Ontology termsGene Ontology 术语 | GO term names and namespaces used while building yeast GMT files.构建 yeast GMT 文件时使用的 GO term 名称和命名空间。 | Gene Ontology go-basic.obo | Attribute the Gene Ontology Consortium and follow current GO resource terms.归属 Gene Ontology Consortium，并遵循 GO 资源当前条款。 |
TAFFISH-derived example packages
TAFFISH 派生示例数据包
rnaseq-yeast-get-data prepares a 24-sample real-mini package from the public project: 12 WT and 12 snf2_KO biological samples, 500k single-end reads per sample, a selected 12-vs-12 gene count matrix, SGD reference files and SGD/GO-derived GMT/background resources. It records the selected biological replicates, all lane accessions, actual download source, fallback status, file checksums and generated package manifests.
rnaseq-yeast-get-data 从该公开项目准备 24 样本 real-mini 数据包：12 个 WT 和 12 个 snf2_KO 生物学样本、每样本 500k single-end reads、选定 12-vs-12 gene count matrix、SGD 参考文件，以及 SGD/GO 派生 GMT/background 资源。它会记录选定生物学重复、全部 lane accession、实际下载来源、fallback 状态、文件 checksum 和生成数据包 manifest。
yeast-snf2-fastq-mini-v1: sampled FASTQs and sample metadata.抽样 FASTQ 和样本元数据。yeast-snf2-counts-medium-v1: selected 12-vs-12 author-derived gene count matrix.选定 12-vs-12 作者派生基因计数矩阵。yeast-reference-sgd-r64.4.1-v1: SGD genome FASTA and matching feature-only annotation.SGD genome FASTA 和匹配 feature-only 注释。yeast-sgd-go-gene-sets-r64.4.1-v1: SGD/GO-derived GMT files and background genes.SGD/GO 派生 GMT 文件和背景基因。
How this relates to the reports
这和报告是什么关系
The HTML reports are generated by taf-rnaseq-standard-flow and are intended to stay data-agnostic enough for ordinary user projects. Therefore the detailed public-data statement lives here and in the data-preparation repository, while each report embeds or links its own methods, commands, versions, manifest and output files.
HTML 报告由 taf-rnaseq-standard-flow 自动生成，需要保持对普通用户项目也适用的通用形态。因此详细公开数据声明放在本页和数据准备仓库中；每份报告本身则内嵌或链接自己的 methods、commands、versions、manifest 和输出文件。