Dear all,

As previously suggested, the first journal club will be on Thursday of next week, here in Maths & Physics building, Lecture Theatre 2, 4pm. This was the most popular time among the respondents.

I’ve set up a web page on Wordpress for this group, which has a “follow” option. The site is https://bioinformaticstasmania.wordpress.com/. The site is in construction but I hope will be a good place for things to begin...

Dr Valerie Hecht has found this paper to consider: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8

See (some of) you then!

Best wishes, Mike A survey of best practices for RNA-seq data analysis

* Ana ConesaEmail authormailto:aconesa@ufl.edu, * Pedro MadrigalEmail authormailto:pm12@sanger.ac.uk, * Sonia Tarazona, * David Gomez-Cabrero, * Alejandra Cervera, * Andrew McPherson, * Michał Wojciech Szcześniak, * Daniel J. Gaffney, * Laura L. Elo, * Xuegong Zhang and * Ali MortazaviEmail authormailto:ali.mortazavi@uci.edu

Genome Biology201617:13 DOI: 10.1186/s13059-016-0881-8 © Conesa et al. 2016 Published: 26 January 2016 Abstract

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.

Michael Charleston Associate Professor in Bioinformatics School of Physical Sciences University of Tasmania AUSTRALIA phone: +61 3 6226 2444

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