Small Rna Downstream Analysis Pipeline

Question

[Newbie]

Hi,

I have 25bp SOLiD Frag data.

Goal is to find novel small rna.

So far I have used SHRiMP2 to align the data with default parameters.

Generally what tools/method/steps are used for further downstream analysis(for e.g. remove duplicates, to remove know RNA etc.)

Thanks a lot.

[Michael]

I had a similar question here, about general ncRNA: Identified Potential Non-Coding Rna, And Then?

[Newbie]

Thanks Michael, James and Shameer for your suggestions. I wish - somebody had good blog post on pipeline. Thanks for your answers and support.

Answer 1

[biobot 0.0.77.a.1099]

You could look at DSAP for inspiration. This paper references three other microRNA pipelines which may be of interest too.

Answer 2

[Khader Shameer]

You could take a look at Infernal and Rfam. They will be a good start to remove known RNA from your results. You can use Infernal program to identify RNA homologs and identify the novel small RNA.