Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC
Creators
- 1. Computational and Systems Biology, Biozentrum, University of Basel
Description
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.
Files
Files
(38.4 GB)
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Additional details
Related works
- References
- 10.1101/195958 (DOI)
Funding
- Swiss National Science Foundation
- NCCR RNA & disease: Understanding the role of RNA biology in disease mechanisms (phase I) 51NF40_141735
- Swiss National Science Foundation
- Regulation of mRNA translation and its relationship with disease processes 31003A_170216