Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • 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

        Previous template Next

        Latest Articles

        Collapse
        • SEQadmin2
          Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
          by SEQadmin2



          Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
          ...
          07-09-2026, 11:10 AM
        • SEQadmin2
          Cancer Drug Resistance: The Lingering Barrier to Rising Survival
          by SEQadmin2



          Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

          There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
          07-08-2026, 05:17 AM
        • GATTACAT
          Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
          by GATTACAT
          Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
          07-01-2026, 11:43 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        UC San Diego Bioengineers Map Gene Function in Human Stem Cells by SEQadmin2
        Started by SEQadmin2, Yesterday, 10:26 AM
        0 responses
        13 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        Yesterday, 10:26 AM  
        New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2
        Started by SEQadmin2, 07-09-2026, 10:04 AM
        0 responses
        26 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        07-09-2026, 10:04 AM  
        Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2
        Started by SEQadmin2, 07-08-2026, 10:08 AM
        0 responses
        16 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        07-08-2026, 10:08 AM  
        Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2
        Started by SEQadmin2, 07-07-2026, 11:05 AM
        0 responses
        33 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        07-07-2026, 11:05 AM  
        View All
        Working...