The median fraction of fragments in cell barcodes that overlap called peaks.
Median fraction of fragments overlapping TSS
The median fraction of fragments in cell barcodes that overlap transcription start sites (TSS).
$estimate_num_of_cell
Estimated number of cells
$median_fragments_percell
Median fragments per cell
$median_frac_peaks
Median fraction of fragments overlapping peaks
$median_frac_tss
Median fraction of fragments overlapping TSS
Beads to cells
(left) Barcoderanks plot
Knee plot of number of fragments overlapping peaks for all the barcodes in the library. This number is used to call cells.
(right) Histogram plot
Histograms of number of beads per droplet.
$plot1
$plot3
Summary
Estimated number of cells
The total number of barcodes identified as cells.
Mean read Pairs per cell
Number of input read pairs divided by the estimated number of cells.
Median fraction of fragments overlapping peaks
The median fraction of fragments in cell barcodes that overlap called peaks.
Mean fraction of fragments overlapping peaks
The mean fraction of fragments in cell barcodes that overlap called peaks.
Median fraction of fragments overlapping TSS
The median fraction of fragments in cell barcodes that overlap transcription start sites (TSS).
Mean fraction of fragments overlapping TSS
The mean fraction of fragments in cell barcodes that overlap transcription start sites (TSS).
Fraction of fragments in cells
Fraction of fragments with a valid barcode that are associated with cell-containing partitions.
Number of peaks
Number of peaks.
Plot
(left) The plot of log10 unique fragment in violin. (middle) The plot of TSS proportion in violin. (right) The plot of FRIP score in violin.
Sample ID
$sampleid
Species
$species
Estimated number of cells
$estimate_num_of_cell
Mean raw read pairs per cell
$mean_rawreads_percell
Median fraction of fragments overlapping peaks
$median_frac_peaks
Mean fraction of fragments overlapping peaks
$mean_frac_peaks
Median fraction of fragments overlapping TSS
$median_frac_tss
Mean fraction of fragments overlapping TSS
$mean_frac_tss
Fraction of fragments in cells
$frac_fragments_incells
Number of peaks
$peaks_number
$plot8
Sequencing
Total number of reads pairs
Total number of read pairs that were assigned to this library in demultiplexing.
Fraction of read pairs with a valid barcode
Fraction of read pairs with barcodes that match the whitelist after barcode correction.
Reads mapped to genome
The number of reads that align to the reference genome.
Mitochondria reads ratio
The number of reads that aligned to the mitochondrial chromosome.
Fraction of nucleosome-free-regions
The fraction of fragments (that passed all filters) overlapping nucleosome-free-regions.
Fraction of fragments mono-nucleosome regions
The fraction of fragments (that passed all filters) overlapping mono-nucleosome regions.
Total number of reads pairs
$read_pairs
Fraction of read pairs with a valid barcode
$frac_valid_barcode
Reads mapped to genome
$map_rate
Mitochondria reads ratio
$mit_rate
Fraction of nucleosome-free-regions
$nc_free_region
Fraction of fragments mono-nucleosome regions
$mono_nc_region
$plot5
Cluster
Left
catter plot of barcodes annotated as cells, colored by automatically computed clusters via graph clustering.
Right
Scatter plot of barcodes annotated as cells, colored by number of fragments in the barcode.
$plot10
$plot11
Targeting
Left
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.
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 TSS. Non-cell and cell barcodes are represented with different colors.
$plot4
$plot6
Cell
Percent of duplicates
Fraction of all the sequenced read pairs that come from cell barcodes and are deemed to be PCR duplicates due to alignment to the same genomic position as another read pair in the library.
Jaccard threshold
Threshold of jaccard index for collapsing bead barcodes to cell barcodes.
Left
Observed median per cell unique fragments as a function of downsampled mean read pairs per cell.
Right
Knee plot of jaccard index score per barcode pair.