Arlequin Input format for Mismatch distribution
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Entering edit mode
6.4 years ago

Hello,

I am trying to get a mismatch distribution of 30 Transposable elements belonging to the same family and present in same species (single plant) using Arlequin.

The '.apr' file I made looks like this: 

[Profile]


     NbSamples=1
              GenotypicData=0 
              DataType=DNA
              LocusSeparator=NONE
        MissingData='?'

[Data]

     [[Samples]]

         SampleName="TE"
           SampleSize=30
           SampleData= {

A01 1 ACGCTGGAGAGATGACGAATTGGAGAGCCCATGAGT------AACAAGTCGCGTCGACCACTACTG---------TAAATTGGGCCTAGACGACGAGCTCTAGAATCTAGGCCCATGACGATGACGAGAC-----------------------------CAAGACCTA--GGGCGGCCACCGACTACG------------------------------------------------------CTAAGAGAGAATCCGGAAGATTTAAGA---ATATTTCCTTATCTC-TTAGATTTAAACCTCGGTCGGCTAG-------GAC---TTGTAGAAATAGAGTTTGTACACCTCTGAAA--AGGCCATCCGCAT---TTTT---------------ACACATAAATCACTTGTAATCATTTGCAAACCGCTTAATAA--CAAACTCTCTTGAGATCTT----------------------CGCTAAGTGTTTCTAATCTCAAGAACTT-----TCAGACCTA-----GAATCATTGACTATTTCAACTGTGCAGGTTTCCACCACTACA----
A02 1 ACGCTGGAGAGATGACGAATTAGAGAGCCCATGAGT------AACAAGTCGCGCCGACCACTACTG---------TAAACTGGGCCTAGCCGACGAGCTGTGGAATCTAGGTCCATGACGATGACGAGAC-----------------------------CAAGACGTA--GGGCGGCCGCCGACTACG------------------------------------------------------CTAAGAGAGAATCTGGAAGATTTAGGA---ATCTTTCCTTATCTC-TTATATTTAAACCTAGGTCGATTAG-------GAC---TTGTAGAAATAGACTTTGTATACCTCTAAAA--AGGCCATCCGCAT---TTTT---------------ACACATAAACAACTTGTAATCATTTCCACACAGCTTAATAA--CAAACTCTCTTGAGATCTT----------------------CGTTAAGTGTCTCTCATCTC-AGAACTT-----TCAGACCTA-----GAATCATTGACTATTTCAACTGTACAGGTTTCCACCACCACACT--
A03 1 -CCACATTGGAAAGAACGAGTCGGGAGCGCATGAGT------AACAAATCACGCCAAACTCTACTA--------TAAGGCTGGGCCTAGAAGACGAGCTCTCGGATTTGGGCCCATGACGAGGACAAGGT-----------------------------CAAGACCTA--AAGGCGGCGCCGACTACG------------------------------------------------------CTGAGAAAGAATCCCGAAGCTTTAGGG---AATCAACCTTATCTATTTAGGCGTAGATCTACGCCGACTTA-------GAC---TTGGATAAATAGACCTAGGATACCTCCAAAA--AGGGGATCCGCAA---TTTT---------------ACACAGAAACTACTTGTAATACTTGCAAAA--TCTTAATAA--CAAACTCTCTTGAGATCTC----------------------CGCT--GTGTTTCTCATCTC-AGAGCTT-----TTAGACCTA----GAAACCATTGACTATTTCAACTGTGCAGGTTTCCACCACCA------
A04 1 -CCACATTGGAAAGAACGAGTCGGGAGCCCACGAGT------AACAAATCACGCCGACCTCTACTA--------TAAGGCTGGGCCTAGAAGACGAGCTCTCGGATTTGGGCCCATGACGAGGACAAGGT-----------------------------CAAGACCTA--AAGGCGGCGCCGACTACG------------------------------------------------------CTGAGAAAGAATCCCAAAGATTTAGGG---ATTCAACCTTATCTCTTTAGGCGTAGACCTAGGCCGACTTA-------GAC---TTGGATAAATAGACCTAGGATACCTCCAAAA---AGGGATCCGCAA---TTTT---------------ACACAGAAACTACTTGTAATACTTGCAAAA--GCTTAATAA--CAAACTCTCTTGAGATCTT----------------------CGCT--GTGTTTCTCATCTC-AGAGCTT-----TCAGACCTA----GAAACCATTGACTATTTCAACTGTGCAAGTTTCCACCACCA------
A05 1 -CCTCATTGGAGAGAACGAGTCGGGAGCCCACGAGT------AACAAGTCACGCCGACCTCTACTA--------TAAGATTGGGCCCAGAAGACGAGCTCTCGGATTTGGGCCCATGACGAGGACGAGGT-----------------------------CAAGACCTA-GAAGCGGCCGCCGACTACG------------------------------------------------------CTGGGGGAGAATCCCGAAGATTCAGGA---ATTCGACCTTATCTCTTTAGGCGTAGACCTAGGCCGACTTA-------GAT---TTGTATAAATAGACCTTGTACACCTCGAAAG--AGGAGATCCGCAA---TTTT---------------ACACATAAACTACTTGTAATATTTGCAAAA--GCTTAATAA-GCAAACTCTCTTGAGATATT----------------------CGCTAGGTGTTTCTCATCTC-AGAGCTT-----TCAGACCTA----G--ACCATTGACTATTTCAACTGTGCAGGTTTCCACCACCACA----
A06 1 -CCTCATTGGAGAGAACGAGTCGGGAGCCCACGAGT------AACAAGTCACGCCGACCTCTATTA--------CAAGATTGGGCCCAGAAGACGAGCTCTCGTATTTGGGCCCATGACGAGGACGAAGT-----------------------------CAAGACCTA-GAAGCGGCCGCCGACTACG------------------------------------------------------CTGGGGGAGAATCCCGAAGATTCAGGA---ATTCGACCTTATCTCTTTAGGCGTAGACCTAGGCCGACTTA-------GAT---TTGTATAAATAGACCTTGTACACCTCGAAAG--AGGGGATCCGTAA---TTTT---------------ACACAGAAACTACTTGTAATATTTGCAAAA--GCTTAATAA-AAAAACTCTCTTGAGATCTT----------------------CGCTAGGTGTTTCTCATCTC-AGAGCTT-----TCAGACCTA----G--ACTATTGACTATTTCAACTGTGCAGGTTTCCACCACCACA----

}

    [[Structure]]

        StructureName="New Edited Structure"
        NbGroups=1

        Group={
            "TE"
        }

When I run the analysis using '.ars' file with mismatch distribution (Tasknumber 4) and 'Estimate parameters of demographic expansion' selected it gives me many errors:

Number of loci for haplotype "A03" is different (255) from that previously defined (571) on line 14
   1 #[ERROR # 1] from function "Population::New_read_gametic_data()" : phenotypes have different number of loci
   2 #[ERROR # 2] from function "Samples::NewRead()" : unable to read sample data
    Problems in reading Samples section... aborting reading  project file.

 

I will be very grateful if someone can help me with the correct method to enter data to get a Mismatch Distribution.

Thanks

 

Mismatch Distribution Arlequin Expansion TE • 4.2k views
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Entering edit mode

Hello rimjhim.roy.ch,

Did you solve the preblem? I' ve just met the same problem as yours. It's like : I converted the phased VCf file with the software PGDspider.

  Number of loci for genotype "Oja01" is different (0) from that previously defined (1001090) on line 15
       1 #[ERROR # 1] from function "Population::New_read_genotypic_data()" : phenotypes have different number of loci
       2 #[ERROR # 2] from function "Samples::NewRead()" : unable to read sample data
        Problems in reading Samples section... aborting reading  project file.

And I'm going to generate the SFS file,I don't know how to deal with the problem.

I'll be very grateful if you can help me about the question!

Thanks!

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Entering edit mode

Zhangshzh_14,

I am having the same problem, has anyone discovered a solution?

Cheers

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