Integration of ENCODE RNAseq and eCLIP Data Sets

Boucas, J.

doi:10.1007/978-1-4939-7540-2_8

Item

ITEM ACTIONSEXPORT

Add to Basket

Local TagsRelease HistoryDetailsSummary

Released

Journal Article

Integration of ENCODE RNAseq and eCLIP Data Sets

MPS-Authors

/persons/resource/persons281221

Boucas, J.
Bioinformatics, Core Facilities, Max Planck Institute for Biology of Ageing, Max Planck Society;

External Resource

https://www.ncbi.nlm.nih.gov/pubmed/29236254
(Any fulltext)

Fulltext (restricted access)

There are currently no full texts shared for your IP range.

Fulltext (public)

There are no public fulltexts stored in PuRe

Supplementary Material (public)

There is no public supplementary material available

Citation

Boucas, J. (2018). Integration of ENCODE RNAseq and eCLIP Data Sets. Methods Mol Biol, 1720, 111-129. doi:10.1007/978-1-4939-7540-2_8.

Cite as: https://hdl.handle.net/21.11116/0000-000B-493A-3

Abstract

During the last decade, the study of mRNA decay has largely benefited from an increasing number of high-throughput assays that emerged from developments in next generation sequencing (NGS) technologies as well as mass spectrometry. While assay-specific data analysis is often reported and software made available many researchers struggle with the overwhelming challenge of integrating data from diverse assays, different sources, and of different formats.We here use Python, R, and bash to analyze and integrate RNAseq and eCLIP data publicly available from ENCODE. Annotation is performed with biomart, motif analysis with MEME and finally a functional enrichment analysis using DAVID. This analysis is centered on KHSRP eCLIP data from K562 cell as well as RNAseq data from KHSRP knockdown and respective mock controls.