HL240

The 120–170 bp raw-size window is supportive only. Dimer-like units have a ≤10-bp central gap. Unreconstructed template matches remain candidates; resolved 11–50 bp inserts are retained. Full-library sizes include expected outer adapters and inferred physical indexes, including units with undetected outer handles. The main profile weights each recovered unit by its modeled full-library length; count-based profiles are expandable. Curves are conditional on sequencing and adapter recovery and do not measure TapeStation fluorescence or NGS molarity.

Chromatin enrichment is not classified. Collision O/E is depth normalized (random baseline 1). Sampling uncertainty remains at low depth. TSS–TES profiles are CPM normalized and visual only.

BED uses zero-based, half-open coordinates. BED6 minus strands are reversed; BED3/4 and dot strands use genomic orientation. Auto uses reference point mode when all retained intervals are 1 bp; otherwise it uses region mode, including mixed-width BED files. You can override this with Plot mode. Reference point mode centers each interval at its midpoint (start + end)/2 and shows ±5 kb in 100 bins without scaling a body. Region mode scales bodies to 100 bins with 50 bins across each 5 kb flank. Exact aligned-base coverage (CIGAR M/= /X only; D/N excluded) is divided by each bin's available genomic width, then CPM uses all eligible primary nuclear alignments in the selected scope. Regions are equally weighted. Duplicate intervals are removed; non-primary and absent-contig regions are skipped and counted. Flanks are clipped to chromosome boundaries; bins entirely beyond the chromosome are missing. SEM is across regions. Assembly identity must be confirmed; chromosome names alone cannot verify it. No data are uploaded to a server.