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  • ekarais
    Junior Member
    • May 2019
    • 2
    #1

    Obtaining the chemistry used from the samfile

    Hello everyone,

    I have some Ecoli reads (PacBio RS) in SAM format, and I want to figure out the specific chemistry used (P6-C4, P4-C2, etc.)

    From this link: https://bioinformatics.stackexchange...equel-bams-hea

    I found out that I could check the BASECALLERVERSION field under @RG in the SAM file. For these reads, the BASECALLERVERSION is 2.3.0.0.140640

    What is the corresponding chemistry?
    More generally, is there list that gives this information for all basecaller versions?
    Tags: chemistry, p6-c4, rs2
  • michaeletoler
    Junior Member
    • Apr 2019
    • 1
    #2
    Nice question. I also like to know.
    Olá, meu nome é Michael E. Toler. Por profissão, eu sou um operador de freio ferroviário, sinal e interruptor. Eu estou trabalhando para uma empresa privada. Paralelamente, estou trabalhando para https://olatcc.com.br/trabalhos-feitos. Esta é uma empresa de escrita online. Aqui minha tarefa é escrever mediante solicitação do cliente. Em vez de trabalhar, sou um amante dos esportes. Eu assisto vários eventos esportivos sempre que tenho tempo.

    Comment

    • SNPsaurus
      Registered Vendor
      • May 2013
      • 525
      #3
      This source https://github.com/PacificBioscience...istryTable.cpp

      Has this table which says that 2.3 basecaller corresponds to P6-C4.

      // BindingKit, SequencingKit, BasecallerVersion, Chemistry

      // RS
      {{"100356300", "100356200", "2.1", "P6-C4"}},
      {{"100356300", "100356200", "2.3", "P6-C4"}},
      {{"100356300", "100612400", "2.1", "P6-C4"}},
      {{"100356300", "100612400", "2.3", "P6-C4"}},
      {{"100372700", "100356200", "2.1", "P6-C4"}},
      {{"100372700", "100356200", "2.3", "P6-C4"}},
      {{"100372700", "100612400", "2.1", "P6-C4"}},
      {{"100372700", "100612400", "2.3", "P6-C4"}},

      // 3.0 ("Dromedary"): S/P1-C1/beta
      {{"100-619-300", "100-620-000", "3.0", "S/P1-C1/beta"}},
      {{"100-619-300", "100-620-000", "3.1", "S/P1-C1/beta"}},

      // 3.1 ("Echidna"): S/P1-C1.1
      {{"100-619-300", "100-867-300", "3.1", "S/P1-C1.1"}},
      {{"100-619-300", "100-867-300", "3.2", "S/P1-C1.1"}},
      {{"100-619-300", "100-867-300", "3.3", "S/P1-C1.1"}},

      // 3.1.1 ("Flea"): S/P1-C1.2
      {{"100-619-300", "100-902-100", "3.1", "S/P1-C1.2"}},
      {{"100-619-300", "100-902-100", "3.2", "S/P1-C1.2"}},
      {{"100-619-300", "100-902-100", "3.3", "S/P1-C1.2"}},
      {{"100-619-300", "100-902-100", "4.0", "S/P1-C1.2"}},
      {{"100-619-300", "100-902-100", "4.1", "S/P1-C1.2"}},

      // 3.2 ("Goat"): S/P1-C1.3
      {{"100-619-300", "100-972-200", "3.2", "S/P1-C1.3"}},
      {{"100-619-300", "100-972-200", "3.3", "S/P1-C1.3"}},
      {{"100-619-300", "100-972-200", "4.0", "S/P1-C1.3"}},
      {{"100-619-300", "100-972-200", "4.1", "S/P1-C1.3"}},

      // 4.0 ("Seabiscuit"); S/P2-C2
      {{"100-862-200", "100-861-800", "4.0", "S/P2-C2"}},
      {{"100-862-200", "100-861-800", "4.1", "S/P2-C2"}},
      {{"100-862-200", "101-093-700", "4.1", "S/P2-C2"}},

      // 5.0 ("Iguana"); S/P2-C2
      {{"100-862-200", "100-861-800", "5.0", "S/P2-C2/5.0"}},
      {{"100-862-200", "101-093-700", "5.0", "S/P2-C2/5.0"}},

      // 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet"); S/P2-C2
      {{"100-862-200", "101-309-500", "5.0", "S/P2-C2/5.0"}},
      // 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet (4 rxn)"); S/P2-C2
      {{"100-862-200", "101-309-400", "5.0", "S/P2-C2/5.0"}},

      // --- SG1/16509P/PA5.0 ---
      // 2.1 binding kit/5.1PA support with ..
      // 5.0 ("Iguana"); S/P2-C2
      {{"101-365-900", "100-861-800", "5.0", "S/P2-C2/5.0"}},
      {{"101-365-900", "101-093-700", "5.0", "S/P2-C2/5.0"}},

      // 5.0.1 ChemRel; Sequel® Binding Kit 2.1; S/P2-C2
      {{"101-365-900", "101-309-500", "5.0", "S/P2-C2/5.0"}}, // Sequel® Sequencing Plate 2.1 Silwet (8 rxn)
      {{"101-365-900", "101-309-400", "5.0", "S/P2-C2/5.0"}}, // Sequel® Sequencing Plate 2.1 Silwet (4 rxn)

      // 5.0.1 ChemRel; Sequel® Binding Kit 3.0; S/P3-C3
      {{"101-500-400", "101-427-500", "5.0", "S/P3-C3/5.0"}}, // Sequel® Sequencing Plate 3.0 (8 rxn)
      {{"101-500-400", "101-427-800", "5.0", "S/P3-C3/5.0"}}, // Sequel® Sequencing Plate 3.0 (4 rxn)

      // 5.0.1 ChemRel; Sequel® Dev Binding Kit; S/P2-C2
      {{"101-490-800", "101-490-900", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel II® Sequencing Plate (4 rxn)
      {{"101-490-800", "101-491-000", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel II® Sequencing Plate (8 rxn)

      // 5.0.1 ChemRel; Sequel® Sequencing Plate 3.1 for Dynamic Loading placeholder (4 rxn)
      {{"101-500-400", "101-646-800", "5.0", "S/P3-C3/5.0"}}, // Sequel® Sequencing Plate 3.1 for Dynamic Loading placeholder

      // 5.0.1 ChemRel; Sequel® Dev Sequencing Plate Dyn Loading (4 rxn)
      {{"101-490-800", "101-644-500", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading

      // 5.0.1 ChemRel; Sequel® Sequencing Plate Dyn Loading (4 rxn)
      {{"101-490-800", "101-717-100", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading

      // 5.0.1 ChemRel; Sequel® Dev Sequencing Plate Dyn Loading (4 rxn)
      {{"101-717-300", "101-644-500", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading
      // 5.0.1 ChemRel; Sequel® Sequencing Plate Dyn Loading (4 rxn)
      {{"101-717-300", "101-717-100", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading

      // 5.0.1 ChemRel; Sequel® Dev Sequencing Plate Dyn Loading (4 rxn)
      {{"101-717-400", "101-644-500", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading
      // 5.0.1 ChemRel; Sequel® Sequencing Plate Dyn Loading (4 rxn)
      {{"101-717-400", "101-717-100", "5.0", "S/P3-C1/5.0-8M"}} // Sequel® Dev Sequencing Plate Dyn Loading
      Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

      Comment

      • SNPsaurus
        Registered Vendor
        • May 2013
        • 525
        #4
        The source code for pbbam (https://github.com/PacificBioscience...istryTable.cpp) has this table, which says that the 2.3 basecaller is for the P6-C4 chemistry.
        // BindingKit, SequencingKit, BasecallerVersion, Chemistry

        // RS
        {{"100356300", "100356200", "2.1", "P6-C4"}},
        {{"100356300", "100356200", "2.3", "P6-C4"}},
        {{"100356300", "100612400", "2.1", "P6-C4"}},
        {{"100356300", "100612400", "2.3", "P6-C4"}},
        {{"100372700", "100356200", "2.1", "P6-C4"}},
        {{"100372700", "100356200", "2.3", "P6-C4"}},
        {{"100372700", "100612400", "2.1", "P6-C4"}},
        {{"100372700", "100612400", "2.3", "P6-C4"}},

        // 3.0 ("Dromedary"): S/P1-C1/beta
        {{"100-619-300", "100-620-000", "3.0", "S/P1-C1/beta"}},
        {{"100-619-300", "100-620-000", "3.1", "S/P1-C1/beta"}},

        // 3.1 ("Echidna"): S/P1-C1.1
        {{"100-619-300", "100-867-300", "3.1", "S/P1-C1.1"}},
        {{"100-619-300", "100-867-300", "3.2", "S/P1-C1.1"}},
        {{"100-619-300", "100-867-300", "3.3", "S/P1-C1.1"}},

        // 3.1.1 ("Flea"): S/P1-C1.2
        {{"100-619-300", "100-902-100", "3.1", "S/P1-C1.2"}},
        {{"100-619-300", "100-902-100", "3.2", "S/P1-C1.2"}},
        {{"100-619-300", "100-902-100", "3.3", "S/P1-C1.2"}},
        {{"100-619-300", "100-902-100", "4.0", "S/P1-C1.2"}},
        {{"100-619-300", "100-902-100", "4.1", "S/P1-C1.2"}},

        // 3.2 ("Goat"): S/P1-C1.3
        {{"100-619-300", "100-972-200", "3.2", "S/P1-C1.3"}},
        {{"100-619-300", "100-972-200", "3.3", "S/P1-C1.3"}},
        {{"100-619-300", "100-972-200", "4.0", "S/P1-C1.3"}},
        {{"100-619-300", "100-972-200", "4.1", "S/P1-C1.3"}},

        // 4.0 ("Seabiscuit"); S/P2-C2
        {{"100-862-200", "100-861-800", "4.0", "S/P2-C2"}},
        {{"100-862-200", "100-861-800", "4.1", "S/P2-C2"}},
        {{"100-862-200", "101-093-700", "4.1", "S/P2-C2"}},

        // 5.0 ("Iguana"); S/P2-C2
        {{"100-862-200", "100-861-800", "5.0", "S/P2-C2/5.0"}},
        {{"100-862-200", "101-093-700", "5.0", "S/P2-C2/5.0"}},

        // 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet"); S/P2-C2
        {{"100-862-200", "101-309-500", "5.0", "S/P2-C2/5.0"}},
        // 5.0.1 ChemRel ("Sequel® Sequencing Plate Silwet (4 rxn)"); S/P2-C2
        {{"100-862-200", "101-309-400", "5.0", "S/P2-C2/5.0"}},

        // --- SG1/16509P/PA5.0 ---
        // 2.1 binding kit/5.1PA support with ..
        // 5.0 ("Iguana"); S/P2-C2
        {{"101-365-900", "100-861-800", "5.0", "S/P2-C2/5.0"}},
        {{"101-365-900", "101-093-700", "5.0", "S/P2-C2/5.0"}},

        // 5.0.1 ChemRel; Sequel® Binding Kit 2.1; S/P2-C2
        {{"101-365-900", "101-309-500", "5.0", "S/P2-C2/5.0"}}, // Sequel® Sequencing Plate 2.1 Silwet (8 rxn)
        {{"101-365-900", "101-309-400", "5.0", "S/P2-C2/5.0"}}, // Sequel® Sequencing Plate 2.1 Silwet (4 rxn)

        // 5.0.1 ChemRel; Sequel® Binding Kit 3.0; S/P3-C3
        {{"101-500-400", "101-427-500", "5.0", "S/P3-C3/5.0"}}, // Sequel® Sequencing Plate 3.0 (8 rxn)
        {{"101-500-400", "101-427-800", "5.0", "S/P3-C3/5.0"}}, // Sequel® Sequencing Plate 3.0 (4 rxn)

        // 5.0.1 ChemRel; Sequel® Dev Binding Kit; S/P2-C2
        {{"101-490-800", "101-490-900", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel II® Sequencing Plate (4 rxn)
        {{"101-490-800", "101-491-000", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel II® Sequencing Plate (8 rxn)

        // 5.0.1 ChemRel; Sequel® Sequencing Plate 3.1 for Dynamic Loading placeholder (4 rxn)
        {{"101-500-400", "101-646-800", "5.0", "S/P3-C3/5.0"}}, // Sequel® Sequencing Plate 3.1 for Dynamic Loading placeholder

        // 5.0.1 ChemRel; Sequel® Dev Sequencing Plate Dyn Loading (4 rxn)
        {{"101-490-800", "101-644-500", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading

        // 5.0.1 ChemRel; Sequel® Sequencing Plate Dyn Loading (4 rxn)
        {{"101-490-800", "101-717-100", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading

        // 5.0.1 ChemRel; Sequel® Dev Sequencing Plate Dyn Loading (4 rxn)
        {{"101-717-300", "101-644-500", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading
        // 5.0.1 ChemRel; Sequel® Sequencing Plate Dyn Loading (4 rxn)
        {{"101-717-300", "101-717-100", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading

        // 5.0.1 ChemRel; Sequel® Dev Sequencing Plate Dyn Loading (4 rxn)
        {{"101-717-400", "101-644-500", "5.0", "S/P3-C1/5.0-8M"}}, // Sequel® Dev Sequencing Plate Dyn Loading
        // 5.0.1 ChemRel; Sequel® Sequencing Plate Dyn Loading (4 rxn)
        {{"101-717-400", "101-717-100", "5.0", "S/P3-C1/5.0-8M"}} // Sequel® Dev Sequencing Plate Dyn Loading
        Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

        Comment

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