De novo route无参路线

rnaseq-denovo-expression-flow

This flow quantifies reads against an assembled transcriptome. It builds a Salmon index from the transcript FASTA, runs per-sample Salmon quantification, merges transcript-level count and TPM matrices, and optionally aggregates to gene or cluster level when an explicit mapping is provided.

这个流程把 reads 定量到组装转录组。它从转录本 FASTA 构建 Salmon 索引，对每个样本运行 Salmon 定量，合并转录本层面的 count 和 TPM 矩阵；当用户显式提供映射时，还可以聚合到 gene 或 cluster 层面。

0.1.0-r1Assembled transcriptome to expression matrices组装转录组到表达矩阵GitHub

Minimal command

最小命令

taf-rnaseq-denovo-expression-flow \
  --samples samples.tsv \
  --transcripts denovo-assembly-out/03_results/transcripts/assembled_transcripts.filtered.fa \
  --outdir denovo-expression-out \
  --threads 8

Input requirements

输入要求

--transcripts

The filtered transcript FASTA from the assembly flow. Transcript identifiers become the default feature IDs in downstream matrices and DE results.

来自组装流程的过滤后转录本 FASTA。转录本 ID 会成为下游矩阵和差异结果的默认特征 ID。

samples.tsv

The same biological FASTQ sample table used by the assembly flow. Paths are resolved relative to the table location.

与组装流程相同的生物学 FASTQ 样本表。路径按样本表所在目录解释。

--tx2gene / --cluster-map

Optional mapping from transcript IDs to known genes or pseudo-gene clusters. Without it, the flow intentionally remains transcript-level.

可选的 transcript 到已知 gene 或 pseudo-gene cluster 映射。没有这个映射时，流程会有意保持转录本层面。

Library protocol

文库协议

Use --library-type A unless the Salmon library type is known and should be forced.

除非明确知道并需要强制 Salmon 文库类型，否则使用默认 --library-type A。

Parameter reference

参数说明

ParameterRequiredDefaultMeaning
--samplesyesnoneFASTQ sample table for quantification.用于表达定量的 FASTQ 样本表。
--transcriptsyesnoneAssembled transcript FASTA, usually assembled_transcripts.filtered.fa.组装转录本 FASTA，通常是 assembled_transcripts.filtered.fa。
--outdiryesnoneDedicated output directory.专用输出目录。
--threadsno2Threads for indexing, Salmon quantification, and summaries.索引构建、Salmon 定量和摘要使用的线程数。
--library-typenoASalmon library type. A lets Salmon infer the protocol.Salmon 文库类型。A 让 Salmon 自动推断协议。
--kmerno31Salmon index k-mer size. Keep the default unless read length or assembly properties require a smaller index.Salmon 索引 k-mer 大小。除非 read 长度或组装特征要求更小索引，否则保留默认。
--trim, --skip-fastqcnooffOptional read preprocessing switches for the quantification run.表达定量运行中的可选 reads 预处理开关。
--tx2gene, --cluster-mapnononeOptional mapping used to aggregate transcript matrices to gene or cluster matrices.可选映射，用于把 transcript 矩阵聚合成 gene 或 cluster 矩阵。
--min-assigned-fragsno10Minimum assigned fragments required per sample. Raise it to fail low-yield quantification early.每个样本要求的最小 assigned fragments。调高可让低产出定量更早失败。

Key outputs

关键输出

  • 03_results/salmon/<sample>/quant.sf
  • 03_results/matrices/transcript_counts.tsv
  • 03_results/matrices/transcript_tpm.tsv
  • 03_results/matrices/gene_counts.tsv and gene_tpm.tsv only when a mapping is supplied
  • 04_reports/quant_files.tsv, 04_reports/expression_summary.tsv, 04_reports/matrix_semantics.tsv, run.manifest.json

How it connects

如何连接

The default downstream count matrix is transcript_counts.tsv. Use it with rnaseq-de-flow --gene-column transcript_id or let rnaseq-standard-flow --mode denovo pass the correct file automatically. If a stable mapping is supplied and gene_counts.tsv is produced, that matrix can be used for gene-level DE.

默认下游计数矩阵是 transcript_counts.tsv。可用 rnaseq-de-flow --gene-column transcript_id 连接，或让 rnaseq-standard-flow --mode denovo 自动传递正确文件。如果提供稳定映射并生成 gene_counts.tsv，则可用于 gene-level DE。