denovo assembly for small rna sequencing

[vishwesh]

Hi,
I am working on small RNA reads for micro RNA analysis. I am using velvet for denovo assembly. Can some one suggest a good tool for denovo assembly for small rna reads.

Regards
Vishwesh

[TiborNagy]

Why do you want to assemble small RNSs? Size of small RNSs are smaller than the read size.

[vishwesh]

I want to make a assembly to for finding existing micro RNA and novels ones also... Since there is no reference genome for the species I deal with I thought I could try to build the hairpin structure of the micro RNA using denovo assembly..

Regards
Vishwesh

[TiborNagy]

I guess you would not find whole hairpins (except if you use a very special library preparation). Even detection of miRNA* is also hard. If you would like to find known miRNAs, align reads agains mirBase.

[vishwesh]

Thanks. Our aim is to find novel micro RNA. Can this be done with denovo assembly?

Vishwesh

[NextGenSeq]

What I would do is assemble to the miRNA database and examine the reads which don't align. Most will be tRNA though.