software . 2018

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;
Open Source English
  • Published: 15 Jan 2018
  • Publisher: Zenodo
Abstract
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&rs...
Subjects
free text keywords: Cleavage and polyadenylation, APA, quantification of poly(A) site usage, regulators of polyadenylation, HNRNPC, RNA-seq, Snakemake
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Open Access
Zenodo
Software . 2018
Provider: Datacite
Open Access
Zenodo
Software . 2018
Provider: Datacite
Open Source
Zenodo
Software . 2018
Provider: Zenodo
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