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QAPA specifications


Unique identifier OMICS_28489
Alternative name Quantification of APA
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes




No version available


  • person_outline Quaid Morris
  • person_outline Benjamin Blencowe

Publication for Quantification of APA

QAPA citations


QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA seq data

Genome Biol
PMCID: 5874996
PMID: 29592814
DOI: 10.1186/s13059-018-1414-4
call_split See protocol

[…] QAPA quantifies APA levels using RNA-seq reads that uniquely map to 3′ UTR sequences demarcated by annotated poly(A) sites in last exons. The development and application of QAPA entailed establishing […]


Physician Awareness of Immune Responses to Polyethylene Glycol‐Drug Conjugates

PMCID: 5866984
PMID: 29383836
DOI: 10.1111/cts.12537

[…] sitivity of detection. The variance is possibly attributed to differences in the sensitivities of the APA‐detection assays used across studies. There currently lacks a standardized assay protocol for quantification of APA, a shortcoming that must be rectified for diagnosis of APA.At present, it is unclear why only a handful of PEGylated drugs appear to suffer from anti‐PEG antibody responses, whil […]


Eps15 membrane binding and bending activity acts redundantly with Fcho1 during clathrin mediated endocytosis

Mol Biol Cell
PMCID: 5007088
PMID: 27385343
DOI: 10.1091/mbc.E16-03-0151

[…] elegans were immobilized and 10 cortical Z-sections (0.2-μm steps) were acquired 23 min after oocyte ovulation in utero (Wang et al., 2014). Individual planes ∼1 μm from the eggshell were chosen for quantification of APA-2 puncta at the cortex. Only puncta that reached a minimal threshold of fluorescence intensity (after background subtraction) were used for quantification. To calculate the relat […]


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QAPA institution(s)
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Vector Institute, Toronto, ON, Canada
QAPA funding source(s)
Supported by an Ontario Graduate Scholarship and a CIHR Frederick Banting and Charles Best Canada Graduate Scholarship, and grants from CIHR (FDN-148434 and MOP125894) and Medicine by Design.

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