Miranda parameters
I am using miRANDA command line How can I use following parameters:
- four or fewer mismatches overall,
- only one or none mismatches in the 5' region of the miRNA (positions 1 to 12)
- no more than two consecutive mismatches in positions 13 to 21
- no mismatches in positions 10 and 11
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While you may want those parameters here is what is possible per the manual page.
so my parameters cannot be achieved?
A quick glance at the manual page appears to indicate that there are no options for position specific restrictions. You may need to run the program and parse the output afterwards to achieve your desired output.