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:
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.
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.