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rndouglas 08-20-2014 11:30 AM

miRNA Discovery
I may be a bit naive, but I'm trying to see if I can identify miRNA-precursors in a new genome assembly I recently made.

I have available to me:
  • de novo assembled genome
  • 1x100bp Illumina total RNA RNAseq
  • Illumina sRNA RNAseq

Is there any program that can whittle down potential miRNA-precursor loci using all three sets of sequences rather than going through everything by hand?

I suppose in my head I see something like:
map 100bp read to genome --> look for sRNAs that bind within the mapped 100bp potential precursor --> analyze the region to see if it looks decent to actually be a miRNA precursor --> add it to my list to go back and verify experimentally someday.

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