https://university.nanostring.com/geomx-academy-ngs-data-analysis-for-rna/1029434
Nanostring University
DSP NGS Readout
DSP Data Analysis
The number of raw read per segment (default - 1000 reads)
The percentage of all reads in a segment that remain after removing adapter sequences (default - 80 percent)
The percentage of all reads in a segment that remain after combining paired end reads that have overlapping sequences (default - 80 percent)
The percentage of all reads in a segment that remain after aligning the stitched reads with the RTS ID barcode from the reference assay (default - 80 percent).
After alignment, deduplication occurs by removing PCR duplicates to create deduplicated reads
Sets the minimum percent of sequencing saturation allowed. The percent of sequencing saturation is calculated as:
1 - (deduplicated reads/aligned reads) x 100
100% sequencing saturation indicates a representative sample, while 0% sequencing saturation indicates that all reads were unique. Values below 50% may need to be resequenced (default - 50 %)
The minimum number of reads per segment from the geometric mean of negative probes (default - 10)
The maximum number of reads in the No Template Control (NTC) well of the 96 well plate that was sequenced. NTC wells contain no sample and thus will indicate if there is contamination in the library prep (default - 1000)
The minimum number of nuclei counted for a segment (default 200)
The minimum area of a segment (default 16000)