{"id":3293,"date":"2024-01-30T19:21:19","date_gmt":"2024-01-30T22:21:19","guid":{"rendered":"https:\/\/sites.usp.br\/smagro\/?page_id=3293"},"modified":"2026-05-17T18:48:09","modified_gmt":"2026-05-17T21:48:09","slug":"minicurso-v","status":"publish","type":"page","link":"https:\/\/sites.usp.br\/smagro\/minicurso-v\/","title":{"rendered":"V – Introdu\u00e7\u00e3o \u00e0 an\u00e1lise de amplicon (short read) para microbiomas"},"content":{"rendered":"\t\t
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Introdu\u00e7\u00e3o \u00e0 an\u00e1lise de amplicon (short read) para microbiomas<\/h1>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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Dra. Caroline Sayuri Nishisaka (CENA)<\/h2>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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  • Carga hor\u00e1ria:<\/strong> 8 h; In\u00edcio 8:00 h <\/li>\n
  • Objetivos:<\/strong> Capacitar o participante a executar um fluxo completo e reprodut\u00edvel de an\u00e1lise de dados de amplicon 16S no R, desde a inspe\u00e7\u00e3o de qualidade e processamento com DADA2 at\u00e9 a integra\u00e7\u00e3o de metadados, constru\u00e7\u00e3o de objetos no phyloseq, filtragens biol\u00f3gicas e an\u00e1lises de diversidade alfa\/beta com testes estat\u00edsticos, resultando em visualiza\u00e7\u00f5es interpret\u00e1veis para gera\u00e7\u00e3o de infer\u00eancias biol\u00f3gicas.<\/li>\n
  • Conte\u00fado:<\/strong> Pr\u00e1tico-te\u00f3rico, com fundamenta\u00e7\u00e3o conceitual m\u00ednima necess\u00e1ria ao longo da execu\u00e7\u00e3o do pipeline.<\/li>\n
  • Programa\u00e7\u00e3o:<\/strong>
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    Hora<\/span><\/p>\n<\/td>\n

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    Descri\u00e7\u00e3o das atividades<\/span><\/p>\n<\/td>\n<\/tr>\n

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    08:30<\/span><\/p>\n

    –<\/span><\/p>\n

    10:00<\/span><\/p>\n<\/td>\n

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    1. Abrir o RStudio e configurar o diret\u00f3rio de trabalho.<\/span><\/p>\n

    \u00b7         <\/span><\/span>Instalar\/carregar pacotes essenciais: Dada2<\/i>, tidyverse<\/i>, ShortRead<\/i>, phyloseq<\/i>.<\/span><\/p>\n

    \u00b7         <\/span><\/span>Importar arquivos FASTQ de exemplo (fornecido).<\/span><\/p>\n

    \u00b7         <\/span><\/span>Rodar plotQualityProfile() para visualizar perfis de qualidade.<\/span><\/p>\n

    2. Discutir e definir par\u00e2metros de filtragem e truncamento com base nos gr\u00e1ficos.<\/span><\/p>\n

    \u00b7         <\/span><\/span>Executar <\/span><\/span>filterAndTrim<\/span><\/i><\/code>()<\/span><\/code> <\/span><\/span>com os par\u00e2metros definidos.<\/span><\/p>\n<\/td>\n<\/tr>\n

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    10:30<\/span><\/b><\/p>\n

    –<\/span><\/b><\/p>\n

    11:00<\/span><\/b><\/p>\n<\/td>\n

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    Coffee break<\/span><\/i><\/b><\/b><\/p>\n<\/td>\n<\/tr>\n

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    11:00<\/span><\/p>\n

    –<\/span><\/p>\n

    12:00<\/span><\/p>\n<\/td>\n

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    1. Rodar o bloco de c\u00f3digos padr\u00e3o DADA2:<\/span><\/p>\n

    \u00b7         <\/span><\/span>learnErrors<\/span><\/i><\/code>()<\/span><\/code><\/p>\n

    \u00b7         <\/span><\/span>dada<\/span><\/i><\/code>()<\/span><\/code><\/p>\n

    \u00b7         <\/span><\/span>mergePairs<\/span><\/i><\/code>()<\/span><\/code><\/p>\n

    \u00b7         <\/span><\/span>makeSequenceTable<\/span><\/i><\/code>()<\/span><\/code><\/p>\n

    \u00b7         <\/span><\/span>removeBimeraDenovo<\/span><\/i><\/code>()<\/span><\/code><\/p>\n

    2. Verificar m\u00e9tricas: porcentagem de reads mantidas em cada etapa.<\/span><\/p>\n

    \u00b7         <\/span><\/span>Exportar tabelas intermedi\u00e1rias para visualiza\u00e7\u00e3o.<\/span><\/p>\n

    3. Rodar taxonomia com assignTaxonomy<\/i>() usando SILVA database.<\/span><\/p>\n

    \u00b7         <\/span><\/span>Usar addSpecies<\/i>() (opcional).<\/span><\/p>\n<\/td>\n<\/tr>\n

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    12:00<\/span><\/b><\/p>\n

    –<\/span><\/b><\/p>\n

    14:00<\/span><\/b><\/p>\n<\/td>\n

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    Intervalo para almo\u00e7o<\/span><\/i><\/b><\/b><\/p>\n<\/td>\n<\/tr>\n

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    14:00<\/span><\/p>\n

    –<\/span><\/p>\n

    15:30<\/span><\/p>\n<\/td>\n

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    1. Carregar metadados reais (arquivo .csv fornecido).<\/span><\/p>\n

    2. Criar objetos do phyloseq<\/i>:<\/span><\/p>\n

    \u00b7         <\/span><\/span>otu_table<\/span><\/i>().<\/span><\/p>\n

    \u00b7         <\/span><\/span>tax_table<\/span><\/i>().<\/span><\/p>\n

    \u00b7         <\/span><\/span>sample_data<\/span><\/i>().<\/span><\/p>\n

    \u00b7         <\/span><\/span>phyloseq<\/span><\/i>().<\/span><\/p>\n

    3. Remover artefatos: sequ\u00eancias mitocondriais, cloroplastos e baixas abund\u00e2ncias.<\/span><\/p>\n

    4. Visualizar primeiros gr\u00e1ficos:<\/span><\/p>\n

    \u00b7         <\/span><\/span>Barplot de abund\u00e2ncia relativa por filo\/classe\/g\u00eanero.<\/span><\/p>\n<\/td>\n<\/tr>\n

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    14:45<\/span><\/b><\/p>\n

    –<\/span><\/b><\/p>\n

    16:15<\/span><\/b><\/p>\n<\/td>\n

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    Coffee break<\/span><\/i><\/b><\/b><\/p>\n<\/td>\n<\/tr>\n

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    16:15<\/span><\/p>\n

    –<\/span><\/p>\n

    16:55<\/span><\/p>\n<\/td>\n

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    1. Calcular diversidade alfa com estimate_richness<\/i>():<\/span><\/p>\n

    \u00b7         <\/span><\/span>Shannon, Simpson, Observed ASVs.<\/span><\/p>\n

    \u00b7         <\/span><\/span>Criar boxplots com ggplot2.<\/i><\/span><\/p>\n

    2. Calcular diversidade beta:<\/span><\/p>\n

    \u00b7         <\/span><\/span>Matriz Bray\u2013Curtis com phyloseq::distance<\/i>().<\/span><\/p>\n

    \u00b7         <\/span><\/span>Ordena\u00e7\u00e3o (PCoA ou NMDS) com ordinate<\/i>().<\/span><\/p>\n

    \u00b7         <\/span><\/span>Plotagens personalizadas usando ggplot2.<\/i><\/span><\/p>\n

    3. Rodar PERMANOVA (adonis2<\/i>) para testar efeitos de vari\u00e1vel foco.<\/span><\/p>\n<\/td>\n<\/tr>\n

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    17:00<\/span><\/p>\n<\/td>\n

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    T\u00e9rmino do minicurso<\/span><\/b><\/p>\n

    \u25cf        <\/span><\/span>Momento final de intera\u00e7\u00e3o, d\u00favidas e feedback <\/i><\/span><\/b><\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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    • \u00a0\u00a0Vagas limitadas:<\/strong>\u00a0Esgotado<\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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      Local: Sala de Bioinform\u00e1tica do Departamento de Gen\u00e9tica \u2013 ESALQ\/USP<\/span><\/span><\/p>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t

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