Small RNA data analysis

[katussa10]

I am analyzing a small RNA data set that we generate from Illumina GAII.
This organism doesn't have a sequenced genome. How can I get rid of rRNA, tRNA, snRNA, and snoRNA, as well as those containing the polyA tail?

[petang]

You can try the DSAP package
http://dsap.cgu.edu.tw.
DSAP use the non-coding RNA database PFam to remove all small RNA populatopms other than microRNA.

[pfranchini]

Hi,
I am planning to generate miRNA data using an Illumina GAII and I am a beginner in the miRNA world. Can you please give some detail of your experimental design? My plan is to prepare 10 different libraries each one tagged with the Illumina index and run them together in the same lanes og the GA. My questions are:
1) is a sequencing kit for the sequencing of 36 bp enough to cover the entire miRNAs length or, because of adapters and primers, I need the single end 75 bp reads (2 sequencing kits)?
2) considering that I multiplex 10 different species in each lane, how many lanes I should use to have a good representation of miRNAs for each species? The species I am working have a genome size of about 1Gb.
I appreciate your help.
Thanks