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  • MISA : Issue with misa

    Hello..

    I am new to this field. I was using MISA combined with primer3 for generating markers. For testing the tool I used the sequence of 'SOPF01000005.1', which is downloaded from ncbi. I used the follwing command to genrate the '.misa' file. It worked fine and I got the 'SOPF01000005.fasta.misa' and 'SOPF01000005.fasta.statistics' as output file, which contains valid data.

    perl misa.pl "SOPF01000005.fasta"

    Now from the above 'SOPF01000005.fasta.misa'. I tried to generate the 'SOPF01000005.fasta.p3in' file using the following command. The file is generated but it has 0 record in it.

    perl p3_in.pl "SOPF01000005.fasta.misa"

    Can anybody help me in this matter.

    Some content of SOPF01000005.fasta.misa
    -----------------------------------------------------------
    ID SSR nr. SSR type SSR size start end
    SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 1 p1 (T)10 10 77 86
    SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 2 p1 (A)10 10 814 823
    SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 3 p2 (TC)11 22 1034 1055
    SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 4 c (T)10c(A)11 22 1304 1325
    SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 5 p2 (AC)9 18 1881 1898
    SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 6 p3 (TCC)5 15 3195 3209
    SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 7 c (T)12gatgaa(T)10 28 4259 4286
    SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 8 p1 (A)11 11 8990 9000
    SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 9 c (A)10gaaacaaagaacaagatt(A)12 40 9207 9246​

    Some content of SOPF01000005.fasta.statistics
    -----------------------------------------------------------​-----


    Specifications
    ==============

    Sequence source file: "SOPF01000005.fasta"

    Definement of microsatellites (unit size / minimum number of repeats):
    (1/10) (2/6) (3/5) (4/5) (5/5) (6/5)

    Maximal number of bases interrupting 2 SSRs in a compound microsatellite: 100



    RESULTS OF MICROSATELLITE SEARCH
    ================================

    Total number of sequences examined: 1
    Total size of examined sequences (bp): 251776
    Total number of identified SSRs: 113
    Number of SSR containing sequences: 1
    Number of sequences containing more than 1 SSR: 1
    Number of SSRs present in compound formation: 13​

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