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...
Median high-quality fragments per cellThe median number of high-quality fragments per cell barcodeTRUE 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.FALSE ...
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 and ...
The red sections are used for local background estimates, with the peak background as the median value across all red sections. Finally, an extension step is performed on the filtered peaks. Cell Ranger ATAC examines all fragments inside a peak, each of which has two cut sites, one at ...
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
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...
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 ...
Generally, quality control (QC) criteria for most of single-cell sequencing technologies are based on the read counts (count depth) and feature counts per barcode [32]. Barcodes with either a low count depth or too high count depth are considered to be low quality cells or doublets, ...
[9,10], to measure the effects of genetic variants in TF binding [11] and to assess changes in the activity of TFs, e.g., during inflammatory responses [12] or fasting conditions [13]. Computational footprinting, which only requires a single open chromatin experiment per cell of interest,...
[9,10], to measure the effects of genetic variants in TF binding [11] and to assess changes in the activity of TFs, e.g., during inflammatory responses [12] or fasting conditions [13]. Computational footprinting, which only requires a single open chromatin experiment per cell of interest,...