Galaxy RNA questions

dog_sparky

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Join Date: Jan 2010

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Galaxy RNA questions

01-07-2010, 07:44 AM

Hi, I have three questions which I hope someone (or more) can help me with. Sorry to post so many questions at once, but I am very new to Galaxy. Let me start with the fact that I am using BED files.

1) I am looking for unique miRNAs from a Drosophila miRNA library, so right off the bat these RNA's should be the approximate right size. Are "Repeats and Variations" the right place to start looking for these RNAs?

2) Is "Intersect" the best way to separate newly discovered miRNAs from previously discovered miRNAs? I am using the up to 22nt long feature.

3) What is the most practical way to differentiate between RNA species? I am referring to: siRNAs (20 t0 26 nt long), piRNAs (26 to 31 nt longs) and snoRNAs (generally 70 to 200 nt long)?

Sorry this is such a long list of questions, but again, I am very new to Galaxy.
Tags: mirna

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