每个GEM well是10X芯片上的一个单独的区室,从barcode池 (barcode whitelist,前面--qc的结果中有,评估barcode测序准确度,进而影响细胞鉴定准确度)中随机获取barcode用于标记细胞。为了保证整合多个文库时barcode不发生冲突,通常会在barcode后面加一个数字,标记其来源的GEM well,如AGACCATTGAGACTTA-1和AGACCATTGAGACTTA-2...
Answer: A barcode whitelist is the list of all known barcode sequences that have been included in the assay kit and are available during library preparation. For example, there are roughly 737,000 cell barcodes in the whitelist for 5' v2 chemistry. Here are the first 10 lines of the corr...
单细胞多组学ATAC- Cell Ranger ARC--count 单细胞多组学ATAC-Cellranger ARC-结果解读之网页报告【有一个系列】 多样本合并: gene很好合并,但是peak不行,必须合在一起call peak才行,所以必须在上游就处理完成; Aggregating Multiple GEM Wells with cellranger-arc aggr 目录 QC 分析流程(基本+高级) 建库原理 ...
and performs aggregation on any combination of Gene Expression and Feature Barcode (Antibody or CRISPR Guide Capture, Cell Multiplexing) data that are present in the individual sample outputs.
Cell Ranger ATAC then performs cell calling on the remainder barcodes. The pipeline subtracts a depth-dependent fixed count from all barcode counts to model whitelist contamination. This fixed count is the estimated number of fragments per barcode that originated from a different GEM, assuming a ...
The cell barcodes whitelist for the v3 and v3.1 chemistries are the same, and it can be found here: 3M-february-2018.txt.gz. This file is copied from the Cell Ranger software (using Cell Ranger v3.1.0 as an example): cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/barco...
AllCellGenITpre-madeSTARreferences are located in/nfs/cellgeni/STAR/. Barcode whitelist files are located in/nfs/cellgeni/STAR/whitelists. By default, all processing is done using 16 CPUs and 128Gb of RAM. Sanger Farm typically has 8 Gb of RAM per core, so 8 CPUs/64Gb RAM, or 16 CP...
拆库时可以加--qc参数输出序列质量情况,保存在outs/qc_summary.json中 (whitelist见aggr部分): 'sample_qc': { 'Sample1': { '5': { 'barcode_exact_match_ratio': 0.9336158258904611, 'barcode_q30_base_ratio': 0.9611993091728814, 'bc_on_whitelist': 0.9447542078230667, ...
导入10X Cell Ranger 软件的内部模块,如constants,h5_constants, 和io,它们包含常量定义、HDF5 文件相关的常量和 I/O 操作函数。 常量定义 SPATIAL_WHITELIST=["odin-5K-v2","visium-v1","visium-v2","visium-v3","visium-v4","visium-v5","omni-v1","omni-hires-v1","omni-pat7-v1","pseudo-xl...
越来越多的同学开始自己尝试做10X单细胞转录组数据分析了,除了Linux的基本命令之外,首先用到的软件是cellranger。失败是成功之母,对一个新手来讲很可能会遇到这样那样的问题。我们该怎么办呢? 确认安装完整性 cellranger是自带了测试数据集的,很小,用来测试很合适。