Aiba

Aleksandra Helwak

Altschul

Anthony J. Travis

Aravin

David Tollervey

Dodt

Field

Filipowicz

Gong

Granneman

Grzegorz Kudla

Hafner

Hansen

Helwak

Jonathan Moody

Kent

Kudla

Langmead

Leung

Licatalosi

Lorenz

Markham

Memczak

Quinlan

Rost

Simpson

Wlotzka

Zhang

Methods

English

PubMed

Associations between proteins and RNA-RNA duplexes are important in post-transcriptional regulation of gene expression. The CLASH (Cross-linking, Ligation and Sequencing of Hybrids) technique captures RNA-RNA interactions by physically joining two RNA molecules associated with a protein complex into a single chimeric RNA molecule. These events are relatively rare and considerable effort is needed to detect a small number of chimeric sequences amongst millions of non-chimeric cDNA reads resulting from a CLASH experiment. We present the "hyb" bioinformatics pipeline, which we developed to analyse high-throughput cDNA sequencing data from CLASH experiments. Although primarily designed for use with Ago CLASH data, hyb can also be used for the detection and annotation of chimeric reads in other high-throughput sequencing datasets. We examined the sensitivity and specificity of chimera detection in a test dataset using the BLAST, BLAST+, BLAT, pBLAT and Bowtie2 read alignment programs. We obtained the most reliable results in the shortest time using a combination of preprocessing with Flexbar and subsequent read-mapping using Bowtie2. The "hyb" software is distributed under the GPL (General Public License) and can be downloaded from http://bifx-core.bio.ed.ac.uk/Tollervey/hyb/

Travis, Anthony J

Moody, Jonathan

Helwak, Aleksandra

Tollervey, David

Kudla, Grzegorz

Edinburgh Research Explorer

Hyb:A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

Aberdeen University Research

Hyb : a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

Crossref

Hyb: A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

Genome Res.

Methods Mol.

https://www.pure.ed.ac.uk/ws/files/14590085/1_s2.0_S1046202313004180_main.pdf

Hyb:A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

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