10x Visium空转数据基础流程还得看官网资料，看完事半功倍

最近需要处理10x Visium空间转录组的数据，所以到官网学习了一番基础分析流程的内容。

Slide Parameters

需要搞清楚数据使用的芯片类型，以便后续需要手动对齐图像及跑流程时设置正确的参数：--slide、--area、--slidefile(设备无法联网时需要)。

https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/image-slide-parameters

Manual Alignment

此步骤为可选项，芯片图片正常的情况下可以直接跳过该步骤，若图片中组织覆盖了四个角的矫正锚点或者遮挡了很多的边框，自动对齐可能不准最好先手动对齐一下图像：

1. Fiducial Alignment
   https://www.10xgenomics.com/support/software/space-ranger/latest/tutorials/inputs/image-fiducial-alignment

2. CytAssist image alignment
   https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/image-cytassist-image-alignment

Run Pipeline

参考基因组索引构建，人和小鼠可直接下载，需要自己构建可参考：

1. Custom References
   https://www.10xgenomics.com/support/software/space-ranger/latest/advanced/custom-references

根据实际情况选择合适的流程及参数：

2. Spaceranger Count
   https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/space-ranger-count

Review Outputs

所有结果文件:

• https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/output-overview

网页报告解读：

• https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/space-ranger-web-summary

空间结果：

• https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs

Software Download

https://www.10xgenomics.com/support/software/space-ranger/downloads