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        "---\n",
        "title: \"Creating a workflow for genome-environment-association analyses with RADseq data\"\n",
        "author: \"Lara Breitkreutz\"\n",
        "format: revealjs\n",
        "editor: visual\n",
        "---"
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      "id": "fe9599b7"
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        "## Project Goal\n",
        "\n",
        "Clearly demonstrate your project goal\n",
        "\n",
        "## Methods\n",
        "\n",
        "::: {.incremental, .scrollable}\n",
        "- Alignment\n",
        "  - Aligned sequences to a reference *Zostera marina* genome using the BWA MEM function in the Burrow-Wheeler Aligner software (Li and Durbin, 2009).\n",
        "  \n",
        "```{.bash}\n",
        "## Aligning\n",
        "\n",
        "# a for loop that aligns each .fq file according to name of sample and outputs a .sam file\n",
        "for i in ${ind_ID};\n",
        "do\n",
        "  bwa mem -t 20 -T 30 $REF $INPUT/${i}.fq > $OUTPUT1/${i}.sam 2>> $REPORT\n",
        "done\n",
        "\n",
        "conda deactivate #deactivate conda env\n",
        "\n",
        "## Sorting\n",
        "conda activate samtools_env\n",
        "\n",
        "# a for loop that sorts each .sam file (using samtools) and creates a .bam file\n",
        "for i in ${ind_ID};\n",
        "do\n",
        "  samtools view -b -q 30 $OUTPUT1/${i}.sam > $OUTPUT1/${i}.bam\n",
        "  samtools sort $OUTPUT1/${i}.bam > $OUTPUT2/${i}.bam\n",
        "  samtools index $OUTPUT2/${i}.bam\n",
        "```\n",
        "\n",
        ":::\n",
        "\n",
        "## Methods\n",
        "\n",
        "::: {.incremental}\n",
        "- GENOTYPING: I will genotype polymorphic loci using the ref_map function in STACKS.\n",
        "  \n",
        "\n",
        "```{bash}\n",
        "\n",
        "\n",
        "```\n",
        "\n",
        "\n",
        ":::\n",
        "\n",
        "## Preliminary results\n",
        "\n",
        "Preliminary Results\n",
        "- Show parts of initial data (could be first few lines etc)\n",
        "- Include a table\n",
        "- Include image\n",
        "- Include plot generated from code\n",
        "- Highlight specific lines of code in code block\n",
        "\n",
        "## Next four weeks\n",
        "\n",
        "Outline of next steps for next 4 weeks"
      ],
      "id": "10654f9e"
    }
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