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Old 09-19-2017, 06:49 AM   #1
sombrajo
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Location: Berlin

Join Date: Sep 2017
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Default RNA-editing pipeline for miRNAs?

Hi everyone,

Apparently my first post was not published so I try again with a more general question.

I'm trying to find a proper pipeline for dealing with miRNA editing. I actually found one which seems to be cited quite often http://genome.cshlp.org/content/22/8/1533.long and they have a detailed protocol describing the steps they follow and even the scripts they use here http://www.tau.ac.il/~elieis/miR_editing/

In theory this protocol is able to find miRNA-editing sites and distinguish them from SNPs, so I'd like to know if anyone has ever followed this pipeline or know of a better one. I cannot make it past step 3 "Mapping the mismatches against the pre-miRNA sequences" as the output result is filled with zeros, as if it was not recognising my input files.

I'm working with SE miRNA-seq data and will update this post if more information is needed. I'm kind of lost here so any help would be greatly appreciated.

Thank you in advance,

J.

P.S. Now my post is duplicated and I can't find a way to delete this one.

Last edited by sombrajo; 09-20-2017 at 06:09 AM. Reason: Duplicated post because the first one was not visible until today, I don't know why...
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mirna-editing, mirna-seq, rna-seq

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