Median high-quality fragments per cell:每个细胞barcode中高质量fragments中位数,取决于测序数深度或细胞类型; 4.3 Library Complexity Metric 文库复杂度相关指标。 Percent duplicates:要求≥30% 该指标用于衡量在测序数据中,高质量read pairs中被认为是PCR扩增重复的比例,即
Median high-quality fragments per cell:每个细胞barcode中高质量fragments中位数,取决于测序数深度或细胞类型; 4.3 Library Complexity Metric 文库复杂度相关指标。 Percent duplicates:要求≥30% 该指标用于衡量在测序数据中,高质量read pairs中被认为是PCR扩增重复的比例,即那些具有有效barcode且比对到相同基因组位置的...
mean raw read pairs per cell:每个细胞的测序深度,单细胞测序如果看测序深度的话一定要看每个细胞的,看总的测序量不一定准,因为每个样本的细胞数不一定一样。 Fraction of high-quality fragments in cells:包含在细胞内的高质量片段,高质量的片段指的是具有barcode,片段可以可以mapping 到基因组上,比对质量大于30...
How does a 25% increase in ATAC median fragments per cell sound? An update to our duplicate marking algorithm is making this possible. Now, read pairs are considered duplicates if they share the same starting position, end position, and cell barcode—previously, only the start a...
Median high-quality fragments per cellThe median number of high-quality fragments per cell barcode. Non-nuclear read pairsFraction of sequenced read pairs that have a valid barcode and map to non-nuclear genome contigs, including mitochondria, with mapping quality > 30. ...
For PCA, Cell Ranger ATAC first normalizes the data to median cut site counts per barcode and log-transform it. The pipeline uses a fast, scalable and memory efficient implementation ofIRLBA(Augmented, Implicitly Restarted Lanczos Bidiagonalization Algorithm) that allows in-place centering and feature...
a–e, Line graphs showing the effect of sequencing depth (×1,000 reads per cell) on unique fragments in peak regions (a), TSS enrichment (b), sequencing efficiency (fraction of reads that are associated with filtered cells, not duplicated and located within a peak region;c), median Seura...
Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of ear
Then, we calculated the median of the p values of these t tests. We applied this subsampling strategy 1001 times and calculated the median of the medians to select the subset of the biggest group to run the DE analysis. For a given subset of cells from the biggest group and the ...
median compared to txci-ATAC-seq.eUMAP visualization of mouse lung nuclei (n = 73,280) integrating two replicates across two loading inputs. Nuclei are colored by their predicted cell type.fUMAP visualization of mouse liver nuclei (n = 63,429) integrating two replicates across two ...