aggr 输出结果
目录概览
saw aggr 分析任务由 --id 参数指定输出文件夹目录。输出结果依据数据类型被分类，主要文件被保存在 /outs下。
分析流程输出的具体文件取决于：
- SAW软件的版本
- 单片样本分析任务的分析处理
- 特定的分析参数设置
- ...
空间基因表达相关
完成 Stereo-seq T FF 或 Stereo-seq N FFPE 的多样本 saw aggr 分析后，outs/ 目录将包含以下文件：
| Directory/File Name | Description |
|---|---|
analysis/ | 下游分析文件目录 |
<id>.binN_1.0.h5mu | This output H5MU is named in the format of |
<id>.binN_1.0.marker_features.csv | Format-integrated differential expression analysis (One vs. remaining Others) results, based on the Leiden clustering of binN. |
<id>.binN_1.0.group_one_vs_other_DEGs_features.csv | Format-integrated differential expression analysis (one vs. remaining others) results were performed within each Leiden cluster. For each specific cluster, it performs a "One vs. Other" comparison between the groups defined by the --deg-group-by (e.g., 'Treatment' vs. 'Control'). |
<id>.binN_1.0.cluster_ratio.csv | Generated after the multi-sample aggregation, pre-processing, and clustering steps. It provides a detailed statistical breakdown of the clustering results, recording the distribution of each cluster across different samples. |
报告和可视化文件
| Directory/File Name | Description |
|---|---|
<id>.report.html | Analysis summary report of metrics and plots in HTML format. |
visualization.tar | StereoMap visualization file to presentation and manual processing. |
<id>.stereo | A manifest file in JSON format includes experiment and pipeline information, basic analysis statistics, and references to image and spatial matrix files in the SAW output visualization file folder. |
visualization.tar
由于内部结果文件本身已处于压缩状态，可视化输出包现已改为生成未压缩的 TAR 归档文件（visualization.tar），而不再使用 gzip 压缩格式（.tar.gz）。此项改动免去了冗余的二次压缩步骤，且在本地计算机上解包数据（以便在 StereoMap 中进行可视化与下游分析）时，大幅提升了解压速度。
可视化 TAR 打包文件整合了 StereoMap 所需的全部输出结果。解包后的具体内容列表如下：
visualization
├── C04042E2.rpi
├── C04042E3.rpi
├── mouse_brain_bin50_compare.bin50_1.0.group_one_vs_other_DEGs_features.csv
├── mouse_brain_bin50_compare.bin50_1.0.h5mu
├── mouse_brain_bin50_compare.bin50_1.0.marker_features.csv
└── mouse_brain_bin50_compare.stereo
.stereo
.stereo 是一个JSON格式的统领文件，里面记录了：
- SAW分析流程的基本信息
- 组织样本的相关信息
- 基本分析统计结果
- StereoMap所需的图像相关和矩阵相关的文件信息
*文件详细介绍在 “输出结果” 下的各部分说明中可以找到