[BioRuby] Workflows: NGS + miRNA

Raoul Bonnal bonnalraoul at ingm.it
Mon Jan 3 12:14:44 UTC 2011

Thank you very much, I'll read all the refs.

On 02/gen/2011, at 02.38, MISHIMA, Hiroyuki wrote:

> 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
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