8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller

Sample

Sample ID	8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller
Sample description	Adult mouse cortex cells
Pipeline version	cellranger-atac-2.1.0
Reference path	‎/mnt/scratch2/cellranger-atac-2.1.0/reference/refdata-cellranger-arc-mm10-2020-A-2.0.0‎
Chemistry	ATAC
Organism	Mus_musculus

Sequencing

Sequenced read pairs

Total number of sequenced read pairs assigned to the sample.

Valid barcodes

Fraction of read pairs with barcodes that match the whitelist after error correction.

Q30 bases in barcode

Fraction of barcode read (i2) bases with Q-score >= 30.

Q30 bases in read 1

Fraction of read 1 bases with Q-score >= 30.

Q30 bases in read 2

Fraction of read 2 bases with Q-score >= 30.

Q30 bases in sample index i1

Fraction of sample index read (i1) bases with Q-score >= 30.

Sequenced read pairs	461,891,018
Valid barcodes	95.5%
Q30 bases in barcode	87.8%
Q30 bases in read 1	94.4%
Q30 bases in read 2	93.4%
Q30 bases in sample index i1	92.7%

Cells

Estimated number of cells

The total number of barcodes identified as cells.

Mean raw read pairs per cell

Total number of read pairs divided by the number of cell barcodes

Fraction of high-quality fragments in cells

Fraction of high-quality fragments with a valid barcode that are associated with cell-containing partitions. High-quality fragments are defined as read pairs with a valid barcode that map to the nuclear genome with mapping quality > 30, are not chimeric and not duplicate.

Fraction of transposition events in peaks in cells

Fraction of transposition events that are associated with cell-containing partitions and fall within peaks. Transposition events are located at both ends of all high-quality fragments. This metric measures the percentage of such events that overlap with peaks.

Median high-quality fragments per cell

The median number of high-quality fragments per cell barcode

Plots

(left) Knee plot of number of fragments overlapping peaks for all the barcodes in the library. This number is used to call cells.

(right) Histograms of number of fragments per cell barcode for non-cells and cells.

Estimated number of cells	7,729
Mean raw read pairs per cell	59,760.77
Fraction of high-quality fragments in cells	93.8%
Fraction of transposition events in peaks in cells	40.4%
Median high-quality fragments per cell	25,749

Cell Clustering

Plots

(left) The plot represents cell-associated barcodes in a 2-D embedding produced by the t-SNE algorithm on dimensionality reduced ATAC counts. The colors show an automated graph clustering analysis which groups together cells that have similar chromatin accessibility profiles.

(right) The same 2D projection is shown, but cell coloring depicts the number of high-quality fragments associated with each barcode.

Library Complexity

Percent duplicates

Fraction of high-quality read pairs that are deemed to be PCR duplicates. A high-quality read-pair is one with mapping quality > 30, that is not chimeric and maps to nuclear contigs. This metric is a measure of sequencing saturation and is a function of library complexity and sequencing depth. More specifically, this is the fraction of high-quality fragments with a valid barcode that align to the same genomic position as another read pair in the library.

Plots

Observed median per cell unique fragments as a function of downsampled mean read pairs per cell.

Percent duplicates

34.3%

Mapping

Confidently mapped read pairs

Fraction of sequenced read pairs with mapping quality > 30

Unmapped read pairs

Fraction of sequenced read pairs that have a valid barcode but could not be mapped to the genome

Non-nuclear read pairs

Fraction of sequenced read pairs that have a valid barcode and map to non-nuclear genome contigs, including mitochondria,with mapping quality > 30.

Fragments in nucleosome-free regions

Fraction of high-quality fragments smaller than 124 basepairs.

Fragments flanking a single nucleosome

Fraction of high-quality fragments between 124 and 296 basepairs.

Plots

Insert size distribution in linear scale.

Confidently mapped read pairs	86.6%
Unmapped read pairs	0.9%
Non-nuclear read pairs	12.1%
Fragments in nucleosome-free regions	45.0%
Fragments flanking a single nucleosome	38.9%

Targeting

Number of peaks

Total number of peaks on primary contigs either detected by the pipeline or input by the user.

Fraction of genome in peaks

Fraction of bases in primary contigs that are defined as peaks.

TSS enrichment score

Maximum value of the transcription-start-site (TSS) profile.The TSS profile is the summed accessibility signal (defined as number of cut sites per base) in a window of 2,000 bases around all the annotated TSSs, normalized by the minimum signal in the window.

Fraction of high-quality fragments overlapping TSS

Fraction of high-quality fragments in cell barcodes that overlap transcription start sites (TSS).

Fraction of high-quality fragments overlapping peaks

Fraction of high-quality fragments in cell barcodes that overlap called peaks.

Plots

(left) TSS profile, as described above.

(right) Scatter plot that represents each barcode as a point. The position on the x-axis reflects the number fragments associated with that barcode, while the position on the y-axis corresponds to the percentage of those fragments that overlap peaks. Non-cell and cell barcodes are represented with different colors.

Number of peaks	176,651
Fraction of genome in peaks	5.5%
TSS enrichment score	10.11
Fraction of high-quality fragments overlapping TSS	24.1%
Fraction of high-quality fragments overlapping peaks	43.7%

8k_mouse_cortex_ATACv2_nextgem_Chromium_Controller - Adult mouse cortex cells

Sample

Sequencing

Cells

Cell Clustering

Library Complexity

Mapping

Targeting