Overview

Sample info

project_id mLN
sample_id mLN_S3
puck_barcode_file_id puck_collection
species human
sequencing_date unknown
investigator unknown
experiment unknown

Run modes

This sample was processed using the following run modes, and run mode variables

Run modes
openst
clean_dge FALSE
count_intronic_reads TRUE
count_mm_reads TRUE
detect_tissue FALSE
mesh_data TRUE
mesh_spot_diameter_um 7
mesh_spot_distance_um 7
mesh_type hexagon
n_beads 1e+05
polyA_adapter_trimming TRUE
spatial_barcode_min_matches 0.1
umi_cutoff 100, 250, 500

Mapping statistics

The sample was mapped using polyA_adapter_trimmed reads. The mapping statistics are shown here for each method:

Mapping mode
polyA_adapter_trimmed
input_reads 45.97
uniq_mapped_reads 36.01 (78.3%)
as.cds 8.87 (19.3%)
as.utr 13.77 (30%)
intronic 2.11 (4.6%)
intergenic 1.44 (3.1%)
ambiguous 9.82 (21.4%)
avg_mapped_length 107.18
multi_mapped_reads 6.51 (14.2%)
unmapped_too_short 2.39 (5.2%)
mapped_to_rRNA 4.01 (8.7%)
Note:
All values, except avg_mapped_length, shown in millions

Summarised metrics over beads

Run modes
openst
median_genes 72
median_pcr 1.11363636363636
median_reads 90
median_umis 81
n_beads 156641
sum_reads 18.33 (1e6)

QC plots

Each of the QC plots we show on a per run mode basis, to see if there are any downstream differences based on the run mode variable settings.

‘Knee’-plot

Below we plot a so called ‘Knee-plot’: on the y-axis is the Cummulative sum of reads, on the x-axis are the bead barcodes sorted by number of reads. For single-cell samples, this plot tells you roughly how many beads are in the sample.

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Umi-cutoff plots

Histogram of metrics over beads

Next we show mertics such as number of UMIs, genes, reads and pcr per physical spot. We further distinguish between each run mode, showing one histogram for each.

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Nucleotide distribution per beads

Next we bin the data based on reads into quartile. For each run_mode the data is divided into 4 beads, by reads. This means, that the first bin will contain beads which account 25% of the reads, the second will contain beads which account for the second 25% of reads and so on.

For each run mode we plot the nucleotide distribution per quartile.

You can pick the run_mode to be shown from the dropdown list

Only not-meshed run_mode(s) are shown

Shannon entropy and string compression

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Spatial QC

openst