mirdeep2 does not give a single hit

potterbond007

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Join Date: Jul 2014

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mirdeep2 does not give a single hit

07-14-2014, 10:41 PM

We do not have a sequencer so I am using the existing list of miRNAs in miRBase to check if any of these miRNAs are present in the Phytopthora genome. I converted the RNA sequences into DNA to match with the genome. mapper.pl says that there are matches but after running mirdeep2.pl, The output does not give me a single hit. Is the protocol I am following acceptable. What could be the mistake that I am making.

Another problem is for the mature sequence present in the organism file, only one or two miRNAs are currently available for Phytopthora. Also for miRNA from similar sequence, I selected some miRNAs from brown algae which is said to be similar to Phytophthora.

Could somebody give me suggestions.
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