Quickstart快速开始

Run the RNA-seq standard flow

运行 RNA-seq 标准流程

Prepare local FASTQ files and metadata. For reference mode, also provide a genome FASTA, matching annotation, and optional offline GMT/background resources. For de novo mode, provide a protein FASTA database and optional protein-to-GO map for annotation-derived enrichment.

先准备本地 FASTQ 和样本元数据。有参模式还需要基因组 FASTA、匹配注释，以及可选离线 GMT/background 资源。无参模式需要蛋白 FASTA 数据库，以及可选 protein-to-GO 映射表，用于注释派生富集。

This page is the short route guide. For production runs and every option in taf-rnaseq-standard-flow, read the official GitHub docs.

本页是快速路线说明。正式分析和 taf-rnaseq-standard-flow 的完整参数解释，请阅读 GitHub 上的正式手册。

Reference mode

有参模式

taf-rnaseq-standard-flow \
  --samples samples.tsv \
  --genome genome.fa \
  --annotation genes.gff3 \
  --metadata metadata.tsv \
  --design '~ condition' \
  --contrast condition:treated:control \
  --gene-sets gene_sets.gmt \
  --background background.tsv \
  --outdir rnaseq-standard-out \
  --threads 8

De novo mode

无参模式

taf-rnaseq-standard-flow \
  --mode denovo \
  --samples samples.tsv \
  --metadata metadata.tsv \
  --design '~ condition' \
  --contrast condition:treated:control \
  --protein-db proteins.faa \
  --go-map protein_go_map.tsv \
  --outdir rnaseq-denovo-standard-out \
  --threads 16 \
  --max-memory 64G

--protein-db and --go-map are not produced by the sequencer. They are biological annotation resources selected by the analyst, often from a related organism, curated proteome, or project-approved database.

--protein-db 和 --go-map 不是测序仪下机数据，而是分析者选择的生物学注释资源，通常来自近缘物种、curated proteome 或项目认可数据库。

Route choices

路线选择

The default reference route uses Salmon/tximport counts for differential expression. Add --route both to generate alignment/count/QC evidence. Add --route both --de-source featurecounts only when DESeq2 should use featureCounts instead of Salmon counts. De novo mode is selected with --mode denovo and is incompatible with the reference alignment/count branch.

默认有参路线使用 Salmon/tximport 计数做差异表达。添加 --route both 可以生成比对、计数和 QC 证据；如果希望 DESeq2 使用 featureCounts 而不是 Salmon 计数，使用 --route both --de-source featurecounts。无参模式通过 --mode denovo 选择，不能与有参比对/计数分支混用。

Primary outputs

主要输出

  • 04_reports/rnaseq_report.html
  • 04_reports/report_interpretation.html
  • 03_results/expression/ or 03_results/denovo_expression/
  • 03_results/de/ and optional 03_results/enrichment/
  • 03_results/plots/png/ and 03_results/plots/pdf/
  • 04_reports/commands.sh, 04_reports/versions.tsv, and run.manifest.json