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Table 1 Comparison of various features of MAAPER, scAPA, and Sierra

From: MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads

 

MAAPER

scAPA

Sierra

Input data type

Bulk RNA-seq or scRNA-seq

scRNA-seq

scRNA-seq

Applicable to multiple samples

Yes

Yes

Yes

PAS resolution

Individual PAS

Range based on read peak

Range based on read peak

PAS identification method

Modeling based on known PASs

De novo

Do novo

Basis for PAS quantification

Cell cluster

Single cell

Single cell

Basis for APA analysis

Cell cluster

Cell cluster

Cell cluster

Individual-based paired test

Yes

No

No