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Old 09-16-2013, 10:41 AM   #1
tjcarr
Junior Member
 
Location: Delaware

Join Date: Apr 2013
Posts: 1
Question MIREAP - optimizing options for different species?

Hello all,

I'm trying to discover novel miRNAs in avian species and I was wondering if anyone has any experience with using MIREAP and customizing the options for non-mammalian genomes? The documentation for MIREAP is sparse but the output is great once you get it working.

There are four options that define the maximum and minimum miRNA sequence length and the maximum and minimum miRNA reference length. The min-max sequence lengths default to 18-26. The min-max reference sequence lengths default to 20-24. My concern is that the numbers don't match up and I'm not sure why. I understand mammalian miRNAs are ~22nt long, but in avian species miRNAs are ~23nt in length. As such, can I move all default parameters up 1nt or do I expand the parameters to include the low and high range (whether this is 20-26 or dependent on sequence length distribution within a sample set).

I just want to make sure I'm squeezing as much out of it without causing issues by tweaking the options too much.
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mireap, mirna identification, mirna-seq

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