miRDeep 2 output score

[RTK45]

Hi,

i would like to know how are computed the score associated with the precursors. Because when i execute miRDeep2.pl i obtain a file precursors.fa_all which contains 900 + precursors and when i execute miRDeep2_core_algorithm.pl (For each potential miRNA precursor input, the miRDeep2 core algorithm either discards it or assigns it a log-odds score that reflects the probability that the precursor is a genuine miRNA) i obtain only 90 precursors

I expected more results, moreover each precursor is associated with a score, for example :

score total -3.4
score for star read(s) -1.3
score for read counts -5.4
score for mfe 1.7
score for randfold 1.6
total read count 1
mature read count 1
loop read count 0
star read count 0

Do you know how the "score total" is computed ? there is no information about this into the documentation page. I want to understand why the other potential precursors have been removed.

Documentation page : http://www.mdc-berlin.de/en/research...mentation.html

Thank you

[RTK45]

Nobody uses miRDeep 2 ?

[bharat_iyengar]

i think its too late now but the scoring formula is given in mirdeep1 paper in nature biotech