miRDeep2

miRDeep home

Parameters used


miRDeep2 version2.0.0.3
Program call/fs/cbsubscb07/storage/jm889//packages/mirdeep2/miRDeep2.pl rhiMic1_reads.fa rhiMic1.fa rhiMic1_reads_vs_genome.arf none /fs/cbsubscb07/storage/jm889/scripts/mirdeep2/data/dmeMature.fa none -t R.microplus
ReadsrhiMic1_reads.fa
GenomerhiMic1.fa
MappingsrhiMic1_reads_vs_genome.arf
Reference mature miRNAsnone
Other mature miRNAs/fs/cbsubscb07/storage/jm889/scripts/mirdeep2/data/dmeMature.fa
SpeciesR.microplus


Survey of miRDeep2 performance for score cut-offs -10 to 10
miRDeep2 scorefor details on how the log-odds score is calculated, see Friedlander et al., Nature Biotechnology, 2008. estimated signal-to-noisefor the given score cut-off, the signal-to-noise ratio is estimated as r = total miRNA hairpins reported / mean estimated false positive miRNA hairpins over 100 rounds of permuted controls. excision gearingthis is the minimum read stack height required for excising a potential miRNA precursor from the genome in this analysis.
101.23
91.13
81.13
71.13
613
513
41.13
313
213
11.33
01.13
-10.53
-20.43
-30.53
-40.63
-50.63
-60.63
-70.73
-80.73
-90.73
-100.83





novel miRNAs predicted by miRDeep2


provisional idthis is a provisional miRNA name assigned by miRDeep2. The first part of the id designates the chromosome or genome contig on which the miRNA gene is located. The second part is a running number that is added to avoid identical ids. The running number is incremented by one for each potential miRNA precursor that is excised from the genome. Clicking this field will display a pdf of the structure, read signature and score breakdown of the reported miRNA. miRDeep2 scorethe log-odds score assigned to the hairpin by miRDeep2 estimated probability that the miRNA candidate is a true positivethe estimated probability that a predicted novel miRNA with a score of this or higher is a true positive. To see exactly how this probability is estimated, mouse over the 'novel miRNAs, true positives' in the table at the top of the webpage. rfam alertthis field indicates if the predicted miRNA hairpin has sequence similarity to reference rRNAs or tRNAs. Warnings in this field should overrule the estimated probability that a reported miRNA is a true positive (previous field). total read countthis is the sum of read counts for the predicted mature, loop and star miRNAs. mature read countthis is the number of reads that map to the predicted miRNA hairpin and are contained in the sequence covered by the predicted mature miRNA, including 2 nts upstream and 5 nts downstream. loop read countthis is the number of reads that map to the predicted miRNA hairpin and are contained in the sequence covered by the predicted miRNA loop, including 2 nts upstream and 5 nts downstream. star read countthis is the number of reads that map to the predicted miRNA hairpin and are contained in the sequence covered by the predicted star miRNA, including 2 nts upstream and 5 nts downstream. significant randfold p-valuethis field indicates if the estimated randfold p-value of the excised potential miRNA hairpin is equal to or lower than 0.05 (see Bonnet et al., Bioinformatics, 2004). miRBase miRNAthis field displays the ids of any reference mature miRNAs for the species that map perfectly (full length, no mismatches) to the reported miRNA hairpin. If this is the case, the reported miRNA hairpin is assigned as a known miRNA. If not, it is assigned as a novel miRNA. If more than one reference mature miRNA map to the miRNA hairpin, then only the id of the miRNA that occurs last in the input file of reference mature miRNAs for the species is displayed. example miRBase miRNA with the same seedthis field displays the ids of any reference mature miRNAs from related species that have a seed sequence identical to that of the reported mature miRNA. The seed is here defined as nucleotides 2-8 from the 5' end of the mature miRNA. If more than one reference mature miRNA have identical seed, then only the id of the miRNA that occurs last in the input file of reference mature miRNAs from related species is displayed. UCSC browserif a species name was input to miRDeep2, then clicking this field will initiate a UCSC blat search of the consensus precursor sequence against the reference genome. NCBI blastnclicking this field will initiate a NCBI blastn search of the consensus precursor sequence against the nr/nt database (non-redundant collection of all NCBI nucleotide sequences). consensus mature sequencethis is the consensus mature miRNA sequence as inferred from the deep sequencing reads. consensus star sequencethis is the consensus star miRNA sequence as inferred from the deep sequencing reads. consensus precursor sequencethis is the consensus precursor miRNA sequence as inferred from the deep sequencing reads. Note that this is the inferred Drosha hairpin product, and therefore does not include substantial flanking genomic sequence as does most miRBase precursors. precursor coordinateThe given precursor coordinates refer do absolute position in the mapped reference sequence
n_contig62011_27337 2.2e+4 44089 44068 0 21 yes blast uacuuugagucgguacgaauccu gauuuguaccgacucuuggcuaggu gauuuguaccgacucuuggcuagguuuuacugaaacuacuuugagucgguacgaauccu n_contig62011:1079..1138:+
n_contig556178_18970 8.3e+2 1637 1361 0 276 yes dme-mir-190 blast agauauguuugauauucuugguu ccaggagucagacauauucuca agauauguuugauauucuugguugugauucugagucagccaggagucagacauauucuca n_contig556178:60..120:+
nb_Contig29231_5451 6.0e+2 1184 1176 0 8 no blast gguccugucgcggacgcca gcugaaucgaggaucgccgagc gcugaaucgaggaucgccgagcgguccugucgcggacgcca nb_Contig29231:1048..1089:+
nb_Contig30400_1707 5.4e+2 1088 1048 32 8 no blast uucgauauaugcggcaaguuuucua gaaacgucuugcuguggccauc uucgauauaugcggcaaguuuucuaaacaguuuguccacaucacauguucgggcacugggaaacgucuugcuguggccauc nb_Contig30400:583..664:-
n_contig158079_18042 3.7e+2 719 702 0 17 yes dme-mir-281-2 blast aagagagcaauccguggacagu ugucauggagucgcucucuuua aagagagcaauccguggacaguaugcaauuaacccugacugucauggagucgcucucuuua n_contig158079:122..183:+
n_contig13489_31589 2.7e+2 580 578 0 2 no blast uauuucgauaaugagguguuggac ccgacaaucacugcccuugacgc ccgacaaucacugcccuugacgcguucuccuuguauuucgauaaugagguguuggac n_contig13489:916..973:+
n_contig711839_16729 2.2e+2 439 127 310 2 no blast ucggugcaguucuggaauuucgg uucaauucccaguagcugcuucacaa uucaauucccaguagcugcuucacaagcuccauucggaaggcaagcuggucguaacgaggcgcucggugcaguucuggaauuucgg n_contig711839:406..492:+
nb_Contig6499_7321 2.1e+2 423 422 0 1 no blast ucaccggggccuuuucgacgag cgcgaaaauguucugauuggca cgcgaaaauguucugauuggcauugauagaauaaauugucaccggggccuuuucgacgag nb_Contig6499:709..769:+
n_contig420038_29592 1.2e+2 259 256 0 3 no blast ugaacugaacauccuaggagau uccuggguucuucgaauuguag uccuggguucuucgaauuguaggaagcauuaugaacugaacauccuaggagau :39..92:
n_contig105211_28088 9.1e+1 188 182 4 2 no blast ugguaguucgucaaccuu auuugauaucuaugcuacc ugguaguucgucaaccuuuagugagucuugauguucacucucaauuugauaucuaugcuacc n_contig105211:165..227:+
n_contig552613_29658 7.9e+1 261 245 0 16 no blast aaaacauauacgucguga uuauuuguggugauugga aaaacauauacgucgugaaaaacguucuuuuauuauuuguggugauugga n_contig552613:1117..1167:+
n_contig359802_29065 6.9e+1 169 166 0 3 no blast aaugauaguaggauguguuugu auaacucccucuacaauuuc auaacucccucuacaauuucagagcgugcaccaaugaaacagucaucuucaaugauaguaggauguguuugu n_contig359802:67..139:+
n_contig593625_32524 6.8e+1 151 145 3 3 no blast ugugaugaaagcguucagaacagca gcaauucguagcgcuuuccca gcaauucguagcgcuuucccaucugcuccaucaauacaguugugccaguuucaugugaugaaagcguucagaacagca n_contig593625:1387..1465:-
n_contig176936_27135 6.8e+1 159 158 0 1 no blast cgaggagacuguguucca aaauuagguuguuuaauau aaauuagguuguuuaauauuuuuguagccagagguaaugcgauuauacgaggagacuguguucca n_contig176936:240..305:+
nb_Contig6499_7317 4.7e+1 100 99 0 1 no blast ucaccggcgcuuuuucgacgag ggcgaaaauguuccgguug ggcgaaaauguuccgguugaauugaauggcugauuugucaccggcgcuuuuucgacgag nb_Contig6499:36..95:+
n_contig256438_17678 4.4e+1 93 89 1 3 yes blast aaugguucgugaggcugcc agcagacuuacaaggacc aaugguucgugaggcugccaaaaaaacaagaacgaguaaugggauuuuagcagacuuacaaggacc n_contig256438:244..310:+
nb_Contig28542_815 3.7e+1 80 78 0 2 no blast guguuggauaucgacgguggauugc gaucuacugauuauggaucugcuaca gaucuacugauuauggaucugcuacagccgcagccgcggaggaaccuucacgagaacggcguguuggauaucgacgguggauugc nb_Contig28542:266..351:+
nb_Contig6499_7323 2.6e+1 52 32 0 20 yes blast ucaccggagccuuuucgacgag cacgaaaauguucugguuggca cacgaaaauguucugguuggcauugaucgaauaauuugucaccggagccuuuucgacgag nb_Contig6499:1047..1107:+
n_contig613339_30790 2.2e+1 46 44 0 2 yes blast ugacaggauauuaugguugggcc aacugaccuaacagccaugcagcgug ugacaggauauuaugguugggcccugagaaacaauucaacugaccuaacagccaugcagcgug n_contig613339:1201..1264:+
n_contig731475_29413 1.8e+1 35 34 0 1 yes blast agggacacucuccguacugga ccagucccaaguguguccuacau agggacacucuccguacuggaggcuccguacauuggagcaauccagucccaaguguguccuacau n_contig731475:593..658:-
n_contig226570_30062 1.2e+1 60 52 6 2 no blast uggaaggaucguuuuucg uaagacggcaauuccaugacu uaagacggcaauuccaugacuaaaggugcggguuuuccuggaaggaucguuuuucg n_contig226570:692..748:-
n_contig103104_22626 4.8 28 28 0 0 yes dme-mir-184 blast cggacggacggacggacg uuuguccauucguuagug uuuguccauucguuagugcguccgggcugacagaugaaagaggcauggacgagcggacggacggacggacg n_contig103104:47..118:-
n_contig282546_18639 4.4 20 16 0 4 no blast aucgacgacuaugaguagcaug ugugacuucgguaguugcugaucuga ugugacuucgguaguugcugaucugacugggagggccucgauccacuucgugugcaaaucgacgacuaugaguagcaug n_contig282546:467..546:+
nb_Contig11022_11932 3.3 15 14 0 1 no blast ugcuagccuugcuuaagaucucgga gaaaaucgaguagcuugauaau ugcuagccuugcuuaagaucucggauuuugguucgaaaaucgaguagcuugauaau nb_Contig11022:1916..1972:+
n_contig378421_21002 3.1 24 23 0 1 yes blast auaacucugagacauuaaga uacucucagagauucccuuau uacucucagagauucccuuauuuaguucucuauaacucugagacauuaaga n_contig378421:342..393:-
nb_Contig28772_2991 2.3 18 17 0 1 no blast acugaucucauuggacgcaaaagu uauuacgucaguggcuaug acugaucucauuggacgcaaaagugacucccggaucacuuauuacgucaguggcuaug nb_Contig28772:202..260:-
nb_Contig28726_1424 1.9 20 20 0 0 yes blast cugcguugcagaucugaccgcc uggucaguugcuucgcagcu cugcguugcagaucugaccgccgccguggucaguugcuucgcagcu nb_Contig28726:262..308:+
n_contig708053_29296 1.8 62 62 0 0 yes blast caggccuuuccagaaugacugc aguuguuuugggaggacacugcu aguuguuuugggaggacacugcuguauguuagacaacaagcaggccuuuccagaaugacugc n_contig708053:345..407:-
nb_Contig28504_14257 1.8 34 34 0 0 yes blast aacgagauagcccacgacugugc acgggguggucucucgggug aacgagauagcccacgacugugcgcgagguuucacaagccgcgacgggguggucucucgggug nb_Contig28504:191..254:-
nb_Contig2841_6144 1.6 21 21 0 0 yes blast uggcaauaaaucugaaggcauucg aauggcauucggaucgaaugccauu aauggcauucggaucgaaugccauuuuguucgcccguguggcaccgcgcgaauggcaauaaaucugaaggcauucg nb_Contig2841:824..900:-
nb_Contig29012_1696 1.6 81 81 0 0 yes blast ucaguaaguguguuugcggauu uccggcagcacauuggcugacg uccggcagcacauuggcugacgcuguuggaagggacgucaguaaguguguuugcggauu nb_Contig29012:637..696:-
n_contig89372_23141 1.5 14 14 0 0 yes blast aggacugaaguggagaaa uuaccacuugagccccgu aggacugaaguggagaaacagacaagcgcaguuuuaccacuugagccccgu :20..71:
n_contig586217_26251 1.2 21 21 0 0 yes blast uagcauauacaguaacucuaau cagaguuacuguauaugcuaca cagaguuacuguauaugcuacauaaagguagcauauacaguaacucuaau n_contig586217:329..379:+
nb_Contig16798_13187 1.1 30 28 2 0 yes blast agcacuggaagcugcacagagaug ucucagagcuccacgcagu agcacuggaagcugcacagagauggcaugccagacagagggaaaugucugcuccaucucagagcuccacgcagu nb_Contig16798:2815..2889:-
n_contig262326_16220 1.1 13 13 0 0 yes blast cagacauacagcagaacgugagcc uaaacgaucugcauguaguu uaaacgaucugcauguaguucacuagguacaugaguggacagacauacagcagaacgugagcc :31..94:
n_contig299214_32376 1.0 11 11 0 0 yes blast ucucagacuugugggggagugcac gggcucugcuucaacguuaagaag gggcucugcuucaacguuaagaagacagcccuucucagacuugugggggagugcac n_contig299214:1914..1970:-
n_contig565854_29358 1.0 13 13 0 0 yes blast caccauaugauugugagagacgc uucuuucauggucuccuaaguuu caccauaugauugugagagacgccuuagaggagguccggaaauuuggacacccgggguucuuucauggucuccuaaguuu n_contig565854:41..121:+
nb_Contig13930_4906 1.0 131 131 0 0 yes blast uuuuggacaagcgaucccgguuuc aacuacgggaauugugcaggaag aacuacgggaauugugcaggaagacgucagguacacgcugacaccaccuuuuuggacaagcgaucccgguuuc nb_Contig13930:968..1041:-
n_contig641172_16641 0.9 18 18 0 0 yes blast cucagucgguagagcaug uuuuuuaccacgggu uuuuuuaccacggguaucggacggccuauugggccgaaaaccucagucgguagagcaug n_contig641172:238..297:+
n_contig138640_24213 0.9 23 23 0 0 yes blast uggcuggauguaggcgcguaag uacgcgccuacauccuacaau uggcuggauguaggcgcguaagccuguacuacgcgccuacauccuacaau n_contig138640:894..944:-
n_contig579332_31472 0.9 16 10 5 1 no blast uaguuguugucgguccuugu caagcacgcgcagcuacua caagcacgcgcagcuacuaaaagcauuauccauggagaagaugaucgcuuguuaguuguugucgguccuugu n_contig579332:1233..1305:-
n_contig593955_23143 0.9 627 558 18 51 yes blast aauccguccgggcgcgcuau gcgcccguagcucaguuuggau gcgcccguagcucaguuuggauagaguaccuggcuacgaaccaggcggucgcgguucgaauccguccgggcgcgcuau n_contig593955:676..754:+
nb_Contig6600_3168 0.8 99 99 0 0 yes blast uugucugguguucugucgggug uccgauagacacguaucuagg uccgauagacacguaucuagguauauguuguaauauauuuugucugguguucugucgggug nb_Contig6600:212..273:-
nb_Contig27628_9414 0.8 85 85 0 0 yes blast cgcaguccaauaguguagagcggug gcguucucacuacgggauuccugg gcguucucacuacgggauuccuggaaaaguguggaaugaaaauaauccacaguuccguguaccacccgcaguccaauaguguagagcggug nb_Contig27628:527..618:-
n_contig00704_32225 0.8 855 789 0 66 yes blast auugggucguuccagugcucgaa uuugggugcgggugcagau auugggucguuccagugcucgaauugugcuucaguuaggggaagaaauaacaaaagguuugggugcgggugcagau n_contig00704:1387..1463:-
nb_Contig7589_9346 0.6 11 10 1 0 yes blast uuccacgacagaaaaggaaugccuu ggcaggccuuucaaagucgugagug uuccacgacagaaaaggaaugccuugccaucaucugggcuacaucaaaguuccgccccuaccuguacggcaggccuuucaaagucgugagug nb_Contig7589:867..959:+
n_contig487400_17268 0.5 19 18 0 1 yes blast cgagaaugucuagacacgagca ugucgacgucuuucucguggau ugucgacgucuuucucguggaugcucugcaaagugugcauaaguuucugcgagaaugucuagacacgagca n_contig487400:180..251:-
nb_Contig29530_787 0.5 35 35 0 0 yes blast ugauauauaaggagauguuggcgca cgccucgcucucuccuuuuuuuauugau cgccucgcucucuccuuuuuuuauugauaugauauauaaggagauguuggcgca nb_Contig29530:442..496:+
n_contig295274_15660 0.5 49 49 0 0 yes blast ggucucaugguguaaugg ugaauaccggugagaccug ggucucaugguguaauggccagcacucugaagcuugaauccagugauucgaguuugaauaccggugagaccug n_contig295274:105..178:+
n_contig428715_16368 0.4 28 27 0 1 no dme-mir-4963 blast uuucucugggacuguccgguug uaucaacaucgcaggaagaga uaucaacaucgcaggaagagacaguguugucugcaauaacaacgcuuauuucucugggacuguccgguug n_contig428715:76..146:-
nb_Contig19294_6367 0.4 24 24 0 0 yes blast cuugucguugaguguuccuuuac uuuggccgcaaguaacacaagcc uuuggccgcaaguaacacaagcccaaguggaaacaccgcuugugcuugucguugaguguuccuuuac nb_Contig19294:332..399:+
n_contig167723_22171 0.3 10 9 1 0 yes blast ucaucgugcacagaauuugcuu gcaggaguuccuguucccgacagca gcaggaguuccuguucccgacagcagccaagcuggcgcagcuuggcagucaucgugcacagaauuugcuu :18..88:
n_contig93725_27579 0.3 52 50 0 2 yes blast uagucacuggggcuaaca aaacaaccaccaacugacu uagucacuggggcuaacaaaacaaccaccaacugacu n_contig93725:631..668:-
n_contig697998_31520 0.2 45 45 0 0 no dme-mir-976 blast guggauuauguagugaaggcag gcuccgcaccauucagcu gcuccgcaccauucagcuucuccccaagaauguggauuauguagugaaggcag n_contig697998:1098..1151:-
n_contig631401_23972 0 27 27 0 0 yes blast ucgguguaguaacaguagcgauau caagcuacuuuuucacacugugu caagcuacuuuuucacacugugucagcucucuggcucgguguaguaacaguagcgauau n_contig631401:488..547:-
n_contig699540_25012 0 13 13 0 0 yes blast uucuggacagaauugauugcau gccuuucacuucucuugguccagguag uucuggacagaauugauugcauugaaagcaguaaaucaugaaaacuacgaguggcuguguaugccuuucacuucucuugguccagguag n_contig699540:147..236:+
n_contig561882_23207 0 222 207 7 8 yes blast aguacuaucauugacugacaaaggg cucacacaaaggucaaucagaggac aguacuaucauugacugacaaagggugccuguauggaaaagacaagcacucacacaaaggucaaucagaggac n_contig561882:95..168:-