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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


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    <subfield code="a">&lt;p&gt;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.&amp;nbsp;It&amp;nbsp;connects the PAQR and KAPAC modules and includes as example&amp;nbsp;input the&amp;nbsp;mapped RNA-seq samples from the study of HNRNPC knock-down in HEK293 cells (originally published on the GEO database with the accession number&amp;nbsp;GSE56010), available also from here:&amp;nbsp;http://www.clipz.unibas.ch/RNAseq_HNRNPC_KD_study.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;PAQR is&amp;nbsp;a method for polyadenylation site usage quantification from RNA sequencing data. KAPAC&amp;nbsp;infers position-dependent activities of sequence motifs on 3&amp;rsquo; end processing from changes in poly(A) site usage between conditions.&lt;/p&gt;</subfield>
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