microRNA sequencing analysis pipeline?

[mrfox]

Hi all,

I am going to analyze the microRNA sequencing data (one control group, one cancer group) but I do not have much experience specifically on miRNA data. We only need to map the reads properly and do not need to detect novel miRNAs at this stage.

I know that miRNAkey or miRanalyzer might be good choices. Does any have suggestions of better tools? Recently published papers on that are also welcome.

Thanks.

[toni_marco]

MicroRNAs from SOLiD machines

Hi,

If you have color-space sequences (SOLiD output) you may find interesting our last paper on the topic. You can use our pipeline to map reads to miRNA sequences downloaded from miRBase. We include a detailed README file with the program.

http://bioinformatics.oxfordjournals.org/content/28/3/318.short

http://www.mirbase.org/tools/seqtrimmap

Do not hesitate to contact me for any question about it.
Cheers,
Toni