CellBin方案可以分为自动流程(SAW)和手动介入方式(StereoMap)。SAW自动运行的CellBin分割结果,其成功率主要与拍摄参数、图像质量等因素高度相关。如果您对自动流程的分割效果不满意,可以采用手动介入的方式,配合SAW获取CellBin结果(后续推文将详细介绍如何使用及操作)。 图5 CellBin多样本数据测试结果展示 a.可公布数据...
python:https://stereopy.readthedocs.io/en/latest/Tutorials/IO.html 发表的文章:Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography 华大的空转测序平台Stereo-seq产出两种数据格式:GEM和GEF,如下: GEM格式 GEM 格式数据由 SAP or SAW (version >= 5.1.3) 软件生成,...
Stereo-seq is a pioneering tool that achieves Nanoscale Resolution: can theoretically achieve a 100% cell capture rate, obtaining more informative and accurate cell clustering results. Stereo-seq provides centimeter-scale panoramic field of view, a maximum field of view of 13 cm x 13 cm, enabling...
时空组学算法工具详解 | Stereo-seq基础数据分析工具SAW 22:00 时空算法工具详解 | 用于Stereo-seq数据的空间单细胞基因表达图谱获取工具STCellbin 51:48 时空组学算法工具详解 | BatchEval Pipeline:多数据集联合分析的批次效应评估工作流程 15:40 时空组学算法工具详解 | Stereopy+SGAE 时空组数据分析和细胞分...
The fastq files from Stereo-seq were processed following the standard pipeline (https://github.com/STOmics/SAW). Initially, the first reads containing coordinate identity (CID) sequences underwent alignment to the designed coordinates of the Stereo-seq chip, based on the results from the first ...
The fastq files from Stereo-seq were processed following the standard pipeline (https://github.com/STOmics/SAW). Initially, the first reads containing coordinate identity (CID) sequences underwent alignment to the designed coordinates of the Stereo-seq chip, based on the results from the first ...
The remaining reads were then aligned to Arabidopsis genome (TAIR10) using STAR (Dobin et al., 2013) and mapped reads with MAPQ 10 were counted and annotated to their corresponding genes using an in-house script (available at https://github.com/BGIResearch/SAW). MID with the same CID ...
记住这里的binsize的设置,后续stereopy分析时需要设置。 二、stereopy的数据来源和安装 stereopy使用的是 GEF 文件文件,这个10X的文件截然不同。这个数据是数据下机后使用STOmics/SAW (github.com),华大自主研发,与数据配套的软件,这里可以类比为spaceranger,可以获得表达矩阵和空间位置的软件。具体使用方法,见链接。
CellBin方案可以分为自动流程(SAW)和手动介入方式(StereoMap)。SAW自动运行的CellBin分割结果,其成功率主要与拍摄参数、图像质量等因素高度相关。如果您对自动流程的分割效果不满意,可以采用手动介入的方式,配合SAW获取CellBin结果(后续推文将详细介绍如何使用及操作)。