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Small Rna Downstream Analysis Pipeline

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.

small solid sequence
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updated by Biostar Biostar • written by Newbie • Newbie

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

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written by Newbie • Newbie

2 answers

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

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written by biobot 0.0.77.a.1099 biobot 0.0.77.a.1099

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.

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written by Khader Shameer Khader Shameer

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