# Alternative polyadenylation

Conventional 3′-end single-cell and spatial transcriptomes were built to count gene expression, yet a small subset of reads carrying untemplated poly(A) tails marks where RNAs actually end. scPolyA uses those tail reads to discover polyadenylation sites de novo, then sets UMI-counting intervals from total-read coverage and reports per-cell or per-spot terminal-site usage, 3′ UTR length and intronic polyadenylation. Across eight single-cell datasets, 63.3% of its sites fell within 25 nt of PolyA_DB 3, above polyApipe, scAPAtrap, Sierra and SCAPE and close to DeepPASS-filtered SCAPTURE.

Conventional 3′-end single-cell and spatial transcriptomes were built to count gene expression, yet a small subset of reads carrying untemplated poly(A) tails marks where RNAs actually end. scPolyA uses those tail reads to discover polyadenylation sites de novo, then sets UMI-counting intervals from total-read coverage and reports per-cell or per-spot terminal-site usage, 3′ UTR length and intronic polyadenylation. Across eight single-cell datasets, 63.3% of its sites fell within 25 nt of PolyA_DB 3, above polyApipe, scAPAtrap, Sierra and SCAPE and close to DeepPASS-filtered SCAPTURE.