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Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC

Gruber, Andreas J.; Schmidt, Ralf; Ghosh, Souvik; Martin, Georges; Gruber, Andreas R.; van Nimwegen, Erik; Zavolan, Mihaela

This archive contains the Snakemake workflow as it was used in the Genome Biology publication. The workflow is provided in a self-contained environment that only requires Conda and Snakemake to be executed. It connects the PAQR and KAPAC modules and includes as example input the mapped RNA-seq samples from the study of HNRNPC knock-down in HEK293 cells (originally published on the GEO database with the accession number GSE56010), available also from here: http://www.clipz.unibas.ch/RNAseq_HNRNPC_KD_study. 

PAQR is a method for polyadenylation site usage quantification from RNA sequencing data. KAPAC infers position-dependent activities of sequence motifs on 3’ end processing from changes in poly(A) site usage between conditions.

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