miRDeep-p "problem in read format"

[PatB]

Hi!!

I am using miRDeep-p since 1 week and everything was OK until I execute the last script. In the manual this script is named miRDeep.pl, but in the zipped file that you can download its name is miRDP.pl. Is this normal? Am I using an incorrect file?

Anyway, if I use this miRDP.pl script it returns me multiple error “problem in read format". I will paste here a little part of my files and my command line in case of someone can help me.

Thank you in advance!

Command line: perl miRDP.pl LC30_miRDeep_signatures LC30_miRDeep_structures > LC30_miRDeep_prediction

LC30_miRDeep_signatures:
ILLUMINA-8C6145:810:MP-SR4:1:2:3109:6128 23 1..23 chr01_0 250 23..45 1e-04 1.00 42.1 Plus / Plus
ILLUMINA-8C6145:810:MP-SR4:1:92:7614:17418 25 1..25 chr01_1000 250 204..228 1e-04 1.00 42.1 Plus / Plus
ILLUMINA-8C6145:810:MP-SR4:1:64:10868:11129 18 1..18 chr01_1001 250 23..40 1e-04 1.00 42.1 Plus / Plus
ILLUMINA-8C6145:810:MP-SR4:1:64:10868:11129 18 1..18 chr01_1002 250 211..228 1e-04 1.00 42.1 Plus / Plus
ILLUMINA-8C6145:810:MP-SR4:1:70:10235:17534 22 1..22 chr01_100 250 207..228 1e-04 1.00 42.1 Plus / Plus
ILLUMINA-8C6145:810:MP-SR4:1:32:8332:13923 24 1..24 chr01_1003 250 23..46 1e-04 1.00 42.1 Plus / Plus
ILLUMINA-8C6145:810:MP-SR4:1:64:13668:14678 24 1..24 chr01_1003 250 23..46 1e-04 1.00 42.1 Plus / Plus
ILLUMINA-8C6145:810:MP-SR4:2:74:14818:9808 24 1..24 chr01_1003 250 23..46 1e-04 1.00 42.1 Plus / Plus
ILLUMINA-8C6145:810:MP-SR4:1:32:8332:13923 24 1..24 chr01_1004 250 205..228 1e-04 1.00 42.1 Plus / Plus
ILLUMINA-8C6145:810:MP-SR4:1:64:13668:14678 24 1..24 chr01_1004 250 205..228 1e-04 1.00 42.1 Plus / Plus

LC30_miRDeep_structures:
>chr01_0 strand:+ excise_beg:22126 excise_end:22375
CAAACGACGACGAGGGAGGUGGCAGGACGCGUCCCACGAGGUGGCUUGUCCAUAGAAGGUGGCAGUUGGCAAUGAAAAAACAAAAAACAGUGGAAACGCAGUCAGCAAUGACAUGGUCCCGAUGGAGAUAGAAACAACAACAAUUAGCUCUGGUGGUGAACACGACCAGGUGAGUGUGUCAAAAUGCGUUUCCGGACAAGGGGUUAUGGUUUCCUUAAACGCGCUGGAGAAACGAAAGACGGAAAAAAGA
....(.((..((.((((.(((......))).)))).))..)).)(((((((........((.(....).))....................(((((((((((((....))))....(((....)))..........(((.((....((.(((((.((....)).)))))))...))))).....))))))))))))))))..(((.(.(((((((..........)).))))).)..))).......... (-64.70)
>chr01_1 strand:+ excise_beg:21943 excise_end:22192
UCUGUUGGUGAACACGAUCGGAUGAGUGCAUGAAAAUGUGUUCCUGGAUAAAAGGGUUUCAGUUUCUUGAACGCGUAGGAGGAAUGAAAGACGGAGAAAAAAUGACUAACACUGUUCAUCGUCUUCGCUAGCCGAAACGAGAAAUAUAAUUGGAGGAAAGAUCGGCGUCGGUGCUUCGGCGACCAAACGACGACGAGGGAGGUGGCAGGACGCGUCCCACGAGGUGGCUUGUCCAUAGAAGGUGGCAGUU
.((((.......(((..(((((((((.((((....))))..((((.......))))(((((((((((((..((..((((((((.(((..(((((.................)))))..)))))))).)))..))...)))))))).....)))))........((((((((....)))))).))...(.((..((.((((.(((......))).)))).))..)).))))))))...))..))))))).. (-66.40)
>chr01_2 strand:+ excise_beg:56028 excise_end:56277
GAGCUUAAGAUUCUGAGAAGCAGUUGAUAGGUAGCCAACUUCUAAAAAUCUGAAAAAGCUGGGUUUCUCAGCUUCUGACUUCUAGUUCAUUUUCUGGACUCUAUAACUACAGCUUCUCAGAAUCUGGACCAAAAGCUGGAUUGUUUAGAUGAGCUUCUGAUUCUAGAAAAAACUGCAGCAGCAAGCUCCCCAAACAGACCCUUAAGAGUCUCGUAGGAAAAAAAAUAAUAUUGGUUGGAUACAUUUGAUU
.......(((((((((((((((((((.((((........(((.........))).((((((((...))))))))......(((((........))))).)))))))))...)))))))))))))).((((((((((......))))....(((((((((.((.(((......))).))))).)))))).((..((((((........)))).)).)).............)))))).............. (-59.10)

[Latifa77]

Hi, do you keep using mirDeep-P? Could you solve your problem and have good results?

[PatB]

Hi!

Yes finally I solve the problem and miRDEEP -p is working properly. It was a mistake in the ID name of the reads. Thanks!

[Latifa77]

I have a question, when you run the script rm_redundant_meet_plant.pl did you see lines with this comment in the terminal??:

Use of uninitialized value in subtraction (-) at ./rm_redundant_meet_plant.pl line 147, <FILE> line 792223

I am trying to uses mirdeep-p but I think my results are not good.