[BioRuby] Workflows: NGS + miRNA

[MISHIMA, Hiroyuki]

Hi all,

Addition to my workflow.

Only miRTRAP requires read alignment generated by Novoalign. Inputs for 
miRExpress are fastq files and miRExpress clips adapters from fastq files.

miRExpress is easy and fast. This one is good for first try.

During using miRExpress, you may find 5'-end variations in mature miRNA 
reads. These prevent accurate alignment. These may be not artifacts. See 
Wu et al. PLoS One, 4, p.e7566, 
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007566 
). Clipping 5'-end variations increase alignment-hits.

MISHIMA, Hiroyuki wrote (2011/01/02 9:54):
> Dear Raoul and the BioRuby list,
>
> My workflow for miRNA analysis using Illumina GAii is like the followings:

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