作用：用 StringTie 把 Gifu RNA-seq 文库分别对 T2T 组装注释与 BRAKER 过滤注释定量，得到下游表达证据。
入口：01_align/align.sh。
输入：``{PROJ_LOTUS_ZC}/data/Gifu/RNA/clean/align.conf（逐行 sample fq1 fq2）；$dir/01.align/<sample>.bam；$ref1={PROJ_LOTUS_ZC}/Gifu/00.assemble_result/Lotus_GifuT2T.gtf、$ref2={PROJ_LOTUS_ZC}/Gifu/09.annotation/06.braker/Gifu_filtered.gtf。
输出：02.stringtie_geta/<sample>/<sample>.gtf+.tsv、03.stringtie_braker/<sample>/ 下同名文件；02.tpm_geta/<sample>.tpm、03.tpm_braker/<sample>.tpm 及各自 all_samples.tpm.tsv（gene_id + TPM，取 .tsv 第 9 列去掉表头后用 join 逐样本合并）。
运行：bash 01_align/align.sh；每样本 stringtie -p 64 -G $ref1 -e -B -o $sample.gtf -A $sample.tsv $dir/01.align/$sample.bam（$ref2 同样式）；索引构建与比对块被注释，须自备 $dir/01.align/<sample>.bam，且 03.*braker 分支依赖 04_braker 的输出。
工具：StringTie -p 64 -G <gtf> -e -B -o <sample>.gtf -A <sample>.tsv；HISAT2 hisat2-build -p 64、hisat2 -p 64 -x <index> -1 <fq1> -2 <fq2> -S <sample>.sam --new-summary；samtools view -H、sort -@ 64、index（比对块已注释）。
English
**Purpose**: Quantify the Gifu RNA-seq libraries with StringTie against the T2T assembly annotation and the BRAKER-filtered annotation, giving the expression evidence used downstream.
**Entry point**: `01_align/align.sh`.
**Inputs**: ``{PROJ_LOTUS_ZC}`/data/Gifu/RNA/clean/align.conf` (read line by line as `sample fq1 fq2`); `$dir/01.align/.bam`; `$ref1=`{PROJ_LOTUS_ZC}`/Gifu/00.assemble_result/Lotus_GifuT2T.gtf` and `$ref2=`{PROJ_LOTUS_ZC}`/Gifu/09.annotation/06.braker/Gifu_filtered.gtf`.
**Outputs**: `02.stringtie_geta//.gtf`+`.tsv` and the same files under `03.stringtie_braker//`; `02.tpm_geta/.tpm`, `03.tpm_braker/.tpm` and each `all_samples.tpm.tsv` (gene_id plus TPM, column 9 of the `.tsv` with the header stripped, merged across samples with `join`).
**Run**: `bash 01_align/align.sh`; per sample `stringtie -p 64 -G $ref1 -e -B -o $sample.gtf -A $sample.tsv $dir/01.align/$sample.bam` (same form with `$ref2`); the index build and alignment blocks are commented out, so `$dir/01.align/.bam` must already exist, and the `03.*braker` branch needs the `04_braker` output.
**Tools**: StringTie `-p 64 -G -e -B -o .gtf -A .tsv`; HISAT2 `hisat2-build -p 64` and `hisat2 -p 64 -x -1 -2 -S .sam --new-summary`; samtools `view -H`, `sort -@ 64`, `index` (the alignment blocks are commented out).