[BioRuby] Workflows: NGS + miRNA (Re: Workflows and Parallelization)

[MISHIMA, Hiroyuki]

Dear Raoul and the BioRuby list,

My workflow for miRNA analysis using Illumina GAii is like the followings:

1) Read alignment using Novoalign. ( http://www.novocraft.com/ ).
It is a proprietary software, but its binary is free for academic use
with several restrictions. The advantage of Novoalign is the function to
remove adapter sequences from each read. Adapter clipping is
indispensable for miRNA analyses because target molecules are always
shorter than read length.

1b) You may be able to use BWA/MAQ instead. Adopter clipping tool such
as Cutadapt ( http://cutadapt.googlecode.com/ ) is available.

2) To find miRBASE-registered miRNAs, I used miRExpress (
http://mirexpress.mbc.nctu.edu.tw/ , Wang et al, BMC Bioinform 10, p328,
2009. http://www.biomedcentral.com/1471-2105/10/328 )

2b) Data analysis. I plotted heatmaps using R. See Ruby et al. (Genome
Res, 17, p1850, 2007. http://genome.cshlp.org/content/17/12/1850.long ).

3) To find potentially novel miRNA, I used miRTRAP
(http://flybuzz.berkeley.edu/miRTRAP.html (Hendrix et al., Genome Biolo,
11, pR39, 2010. http://genomebiology.com/2010/11/4/R39 ).

The workflow may have to be updated. Hopefully, it will help you.

Thanks,
Hiro.

Raoul Bonnal wrote (2010/12/23 18:47):
> Actually the focus of my institute is mainly on mirna, so I'm also
> interested on techniques for analyzing NGS(illumina) and microRNA.

-- 
MISHIMA, Hiroyuki, DDS, Ph.D.
COE Research Fellow
Department of Human Genetics
Nagasaki University Graduate School of Biomedical Sciences