diff --git a/doc/2023_09_18_presentation.qmd b/doc/2023_09_18_presentation.qmd
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+---
+title: "Kmer diff"
+author: "laurent modolo"
+format:
+ revealjs:
+ transition: none
+ format:
+ highlight-style: monokai
+ theme: white
+ footer: "laurent.modolo@ens-lyon.fr"
+ slide-number: c/t
+ fontsize: 22pt
+revealjs-plugins:
+ - pointer
+---
+
+## Background
+
+The Delattre team’s studies, *Mesorhabditis worms*, some species of which present
+atypical reproduction mechanisms.
+
+In a previous paper: *Males as somatic investment in a parthenogenetic nematode* [DOI: 10.1126/science.aau0099](https://doi.org/10.1126/science.aau0099),
+we characterized contigs of a *de novo* genome assembly of *M. belaris* as
+
+
+:::: {.columns}
+::: {.column width="40%"}
+- <span style="color:blue;">Autosomal</span> chromosomes
+- <span style="color:red;">X</span> chromosome
+- <span style="color:green;">Y</span> chromosome
+:::
+
+::: {.column width="60%"}
+{width=350px}
+:::
+
+::::
+
+## Goal
+
+From raw sequencing data of male and female individuals, we want to identify $k$-mers corresponding to :
+
+- <span style="color:blue;">Autosomal</span> chromosomes
+- <span style="color:red;">X</span> chromosome, if present
+- <span style="color:green;">Y</span> chromosome, if present
+
+<div style="text-align: center">**We can study the chromosomal system without an assembly**</div>
+
+## Phylogeny
+
+
+
+## Kmer-diff
+
+A nextflow pipeline to analyze the $k$-mer content of fastq files
+
+1. preprocess the fastq files
+2. count the $k$-mers of each file
+3. merge the counts to get a table of male and female $k$-mers counts
+3. test the sexual models
+4. identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> $k$-mers
+
+## Kmer-diff
+
+
+
+## Preprocessing
+
+**preprocess the fastq files**
+
+Important for the clustering analysis:
+
+- subsample to have the same number of reads between male and female
+
+Important for the $k$-mer counting
+
+- split the fastq files into manageable size files ($10ˆ6$ reads per files)
+
+## $k$-mer count
+
+[fastqkmer](https://github.com/angelovangel/fastkmers)
+
+```
+fastkmers -k 12 file.fastq > file.csv
+```
+
+Run a **sliding window** of size $12$ by step of $1$ along the reads counting all the occurrences of each $k$-mers
+
+We have the letters: $A,C,T,G$ and $N$
+
+<div style="text-align: center">$244,140,625$ possible $k$-mers</div>
+
+We split the fastq files into $\sim$ $1400$ subfiles of $10^6$ reads.
+
+## Merging the $k$-mers
+
+$\sim$ $1400$ splits of $10^6$ reads $\rightarrow$ $1400$ csv files
+
+:::: {.columns}
+::: {.column width="50%"}
+
+- large number of $k$-mers
+- Unordered
+- not the same $k$-mers a present in every files
+
+[mergekmer](https://gitbio.ens-lyon.fr/LBMC/Delattre/mergekmer) a small rust program that builds a **suffix tree** of the $k$-mer
+:::
+
+::: {.column width="50%"}
+
+
+
+:::
+::::
+
+## Merging the $k$-mers
+
+[mergekmer](https://gitbio.ens-lyon.fr/LBMC/Delattre/mergekmer) a small rust program that build a **suffix tree** of the $k$-mer
+
+:::: {.columns}
+::: {.column width="50%"}
+
+```
+merge fastkmers output
+
+Usage: mergekmer [OPTIONS] --output <OUTPUT>
+
+Options:
+ -c, --csv <CSV>... list of csv files
+ -o, --output <OUTPUT> merged csv file
+ -c, --collate collate csv file
+ -h, --help Print help
+ -V, --version Print version
+```
+
+Each leaf of the tree contains the number of $k$-mers
+
+The tree traversal is easy to compute with a recursive function
+
+**we can merge the counts of a given sex for each specie**
+
+:::
+::: {.column width="50%"}
+
+:::
+::::
+
+## Merging the $k$-mers
+
+:::: {.columns}
+::: {.column width="50%"}
+
+```
+merge fastkmers output
+
+Usage: mergekmer [OPTIONS] --output <OUTPUT>
+
+Options:
+ -c, --csv <CSV>... list of csv files
+ -o, --output <OUTPUT> merged csv file
+ -c, --collate collate csv file
+ -h, --help Print help
+ -V, --version Print version
+```
+
+In the `--collate` version each leave contains a list of the count of the $k$-mers in the female or the male of a specie.
+
+**we can fuse the counts of the male and female for each specie**
+
+
+:::
+::: {.column width="50%"}
+
+:::
+::::
+
+## Test the sexual model
+
+**We have the following possible models**
+
+
+:::: {.columns}
+::: {.column width="33%"}
+
+- <span style="color:red;">X</span><span style="color:green;">Y</span> system
+
+
+
+:::
+::: {.column width="33%"}
+
+- <span style="color:red;">X</span>O system
+
+
+:::
+::: {.column width="33%"}
+
+- OO system
+
+
+
+:::
+::::
+
+## Test the sexual model
+
+:::: {.columns}
+::: {.column width="33%"}
+
+- <span style="color:red;">X</span><span style="color:green;">Y</span> system
+
+
+
+:::
+::: {.column width="33%"}
+
+- <span style="color:red;">X</span>O system
+
+
+:::
+::: {.column width="33%"}
+
+- OO system
+
+
+
+:::
+::::
+
+- A cluster with mean male $=$ mean female
+- A cluster above the diagonal
+- A cluster below the diagonal
+
+
+## Test the sexual model
+
+:::: {.columns}
+::: {.column width="25%"}
+
+**data**
+
+
+
+:::
+::: {.column width="25%"}
+
+**XY model**
+
+
+
+:::
+::: {.column width="25%"}
+
+**XO model**
+
+
+:::
+::: {.column width="25%"}
+
+**OO model**
+
+
+
+:::
+::::
+:::: {.columns}
+::: {.column width="50%"}
+
+
+Bayesian information criterion (BIC)
+
+
+
+:::
+::: {.column width="50%"}
+
+Loglikelihood
+
+
+
+:::
+::::
+
+
+## identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> $k$-mers
+
+:::: {.columns}
+::: {.column width="50%"}
+
+
+
+:::
+::: {.column width="50%"}
+
+- Can be used to compare model
+- Not sensitive enough
+- Cannot be used to classify individual $k$-mers
+
+:::
+::::
+
+## identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> $k$-mers
+
+
+:::: {.columns}
+::: {.column width="75%"}
+
+
+:::
+::: {.column width="25%"}
+
+- Can choose the prior for each cluster (mean and shape)
+- Can choose the prior for the proportion between <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span>
+- Can choose the weight of each prior compared to the data
+
+:::
+::::
+
+## identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> $k$-mers
+
+
+:::: {.columns}
+::: {.column width="75%"}
+
+
+:::
+::: {.column width="25%"}
+
+- Can choose the prior for each cluster (mean and shape)
+- Can choose the prior for the proportion between <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span>
+- Can choose the weight of each prior compared to the data
+
+:::
+::::
+
+## identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> $k$-mers
+
+:::: {.columns}
+::: {.column width="75%"}
+
+
+:::
+::: {.column width="25%"}
+
+- Can choose the prior for each cluster (mean and shape)
+- Can choose the prior for the proportion between <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span>
+- Can choose the weight of each prior compared to the data
+
+:::
+::::
+
+## Count problem
+
+:::: {.columns}
+::: {.column width="75%"}
+
+
+:::
+::: {.column width="25%"}
+
+- The coverage is not the same between the male and the female
+
+:::
+::::
+
+## Kmer-diff
+
+A nextflow pipeline to analyze the $k$-mer content of fastq files
+
+1. preprocess the fastq files
+ - **subsample to have the same number of reads between male and female**
+2. count the $k$-mers of each file
+3. merge the counts to get a table of male and female $k$-mers counts
+3. test the sexual models
+4. identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> $k$-mers
\ No newline at end of file
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diff --git a/doc/presentation.html b/doc/presentation.html
new file mode 100644
index 0000000000000000000000000000000000000000..2d3a0de27de638e3691d08ebf9c38f9aa38de3ee
--- /dev/null
+++ b/doc/presentation.html
@@ -0,0 +1,991 @@
+<!DOCTYPE html>
+<html lang="en"><head>
+<script src="presentation_files/libs/clipboard/clipboard.min.js"></script>
+<script src="presentation_files/libs/quarto-html/tabby.min.js"></script>
+<script src="presentation_files/libs/quarto-html/popper.min.js"></script>
+<script src="presentation_files/libs/quarto-html/tippy.umd.min.js"></script>
+<link href="presentation_files/libs/quarto-html/tippy.css" rel="stylesheet">
+<link href="presentation_files/libs/quarto-html/light-border.css" rel="stylesheet">
+<link href="presentation_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
+<link href="presentation_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
+ <meta name="generator" content="quarto-1.3.450">
+
+ <meta name="author" content="laurent modolo">
+ <title>Kmer diff</title>
+ <meta name="apple-mobile-web-app-capable" content="yes">
+ <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
+ <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
+ <link rel="stylesheet" href="presentation_files/libs/revealjs/dist/reset.css">
+ <link rel="stylesheet" href="presentation_files/libs/revealjs/dist/reveal.css">
+ <style>
+ code{white-space: pre-wrap;}
+ span.smallcaps{font-variant: small-caps;}
+ div.columns{display: flex; gap: min(4vw, 1.5em);}
+ div.column{flex: auto; overflow-x: auto;}
+ div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+ ul.task-list{list-style: none;}
+ ul.task-list li input[type="checkbox"] {
+ width: 0.8em;
+ margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
+ vertical-align: middle;
+ }
+ </style>
+ <link rel="stylesheet" href="presentation_files/libs/revealjs/dist/theme/quarto.css">
+ <link href="presentation_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
+ <link href="presentation_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
+ <link href="presentation_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
+ <link href="presentation_files/libs/revealjs/plugin/reveal-pointer/pointer.css" rel="stylesheet">
+ <link href="presentation_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
+ <style type="text/css">
+
+ .callout {
+ margin-top: 1em;
+ margin-bottom: 1em;
+ border-radius: .25rem;
+ }
+
+ .callout.callout-style-simple {
+ padding: 0em 0.5em;
+ border-left: solid #acacac .3rem;
+ border-right: solid 1px silver;
+ border-top: solid 1px silver;
+ border-bottom: solid 1px silver;
+ display: flex;
+ }
+
+ .callout.callout-style-default {
+ border-left: solid #acacac .3rem;
+ border-right: solid 1px silver;
+ border-top: solid 1px silver;
+ border-bottom: solid 1px silver;
+ }
+
+ .callout .callout-body-container {
+ flex-grow: 1;
+ }
+
+ .callout.callout-style-simple .callout-body {
+ font-size: 1rem;
+ font-weight: 400;
+ }
+
+ .callout.callout-style-default .callout-body {
+ font-size: 0.9rem;
+ font-weight: 400;
+ }
+
+ .callout.callout-titled.callout-style-simple .callout-body {
+ margin-top: 0.2em;
+ }
+
+ .callout:not(.callout-titled) .callout-body {
+ display: flex;
+ }
+
+ .callout:not(.no-icon).callout-titled.callout-style-simple .callout-content {
+ padding-left: 1.6em;
+ }
+
+ .callout.callout-titled .callout-header {
+ padding-top: 0.2em;
+ margin-bottom: -0.2em;
+ }
+
+ .callout.callout-titled .callout-title p {
+ margin-top: 0.5em;
+ margin-bottom: 0.5em;
+ }
+
+ .callout.callout-titled.callout-style-simple .callout-content p {
+ margin-top: 0;
+ }
+
+ .callout.callout-titled.callout-style-default .callout-content p {
+ margin-top: 0.7em;
+ }
+
+ .callout.callout-style-simple div.callout-title {
+ border-bottom: none;
+ font-size: .9rem;
+ font-weight: 600;
+ opacity: 75%;
+ }
+
+ .callout.callout-style-default div.callout-title {
+ border-bottom: none;
+ font-weight: 600;
+ opacity: 85%;
+ font-size: 0.9rem;
+ padding-left: 0.5em;
+ padding-right: 0.5em;
+ }
+
+ .callout.callout-style-default div.callout-content {
+ padding-left: 0.5em;
+ padding-right: 0.5em;
+ }
+
+ .callout.callout-style-simple .callout-icon::before {
+ height: 1rem;
+ width: 1rem;
+ display: inline-block;
+ content: "";
+ background-repeat: no-repeat;
+ background-size: 1rem 1rem;
+ }
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+ height: 0.9rem;
+ width: 0.9rem;
+ display: inline-block;
+ content: "";
+ background-repeat: no-repeat;
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+ .callout-title {
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+ }
+
+ .callout-icon::before {
+ margin-top: 1rem;
+ padding-right: .5rem;
+ }
+
+ .callout.no-icon::before {
+ display: none !important;
+ }
+
+ .callout.callout-titled .callout-body > .callout-content > :last-child {
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+ }
+
+ .callout.callout-titled .callout-icon::before {
+ margin-top: .5rem;
+ padding-right: .5rem;
+ }
+
+ .callout:not(.callout-titled) .callout-icon::before {
+ margin-top: 1rem;
+ padding-right: .5rem;
+ }
+
+ /* Callout Types */
+
+ div.callout-note {
+ border-left-color: #4582ec !important;
+ }
+
+ div.callout-note .callout-icon::before {
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+
+ div.callout-note.callout-style-default .callout-title {
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+ div.callout-important {
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+ }
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+
+<section id="title-slide" class="quarto-title-block center">
+ <h1 class="title">Kmer diff</h1>
+
+<div class="quarto-title-authors">
+<div class="quarto-title-author">
+<div class="quarto-title-author-name">
+laurent modolo
+</div>
+</div>
+</div>
+
+</section>
+<section id="background" class="slide level2">
+<h2>Background</h2>
+<p>The Delattre teams studies, <em>Mesorhabditis worms</em>, some species of which present atypical reproduction mechanisms.</p>
+<p>In a previous paper: <em>Males as somatic investment in a parthenogenetic nematode</em> <a href="https://doi.org/10.1126/science.aau0099">DOI: 10.1126/science.aau0099</a>, we caracterized contigs of a <em>de novo</em> genome assembly of <em>M. belaris</em> as</p>
+<div class="columns">
+<div class="column" style="width:40%;">
+<ul>
+<li><span style="color:blue;">Autosomal</span> chromosomes</li>
+<li><span style="color:red;">X</span> chromosome</li>
+<li><span style="color:green;">Y</span> chromosome</li>
+</ul>
+</div><div class="column" style="width:60%;">
+<p><img data-src="./img/science_figure.png" width="350"></p>
+</div>
+</div>
+</section>
+<section id="goal" class="slide level2">
+<h2>Goal</h2>
+<p>From raw sequencing data of male and female individuals, we want to identify <span class="math inline">\(k\)</span>-mers corresponding to :</p>
+<ul>
+<li><span style="color:blue;">Autosomal</span> chromosomes</li>
+<li><span style="color:red;">X</span> chromosome, if present</li>
+<li><span style="color:green;">Y</span> chromosome, if present</li>
+</ul>
+<div style="text-align: center">
+<strong>We can study the chromosomal system without an assembly</strong>
+</div>
+</section>
+<section id="phylogeny" class="slide level2">
+<h2>Phylogeny</h2>
+
+<img data-src="./img/phylogeny.png" class="r-stretch"></section>
+<section id="kmer-diff" class="slide level2">
+<h2>Kmer-diff</h2>
+<p>A nextflow pipeline to analyse the <span class="math inline">\(k\)</span>-mer content of fastq files</p>
+<ol type="1">
+<li>preprocess the fastq files</li>
+<li>count the <span class="math inline">\(k\)</span>-mers of each file</li>
+<li>merge the counts to get a table of male and female <span class="math inline">\(k\)</span>-mers counts</li>
+<li>test the sexual models</li>
+<li>identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> <span class="math inline">\(k\)</span>-mers</li>
+</ol>
+</section>
+<section id="kmer-diff-1" class="slide level2">
+<h2>Kmer-diff</h2>
+
+<img data-src="./img/flowchart.png" class="r-stretch"></section>
+<section id="preprocessing" class="slide level2">
+<h2>Preprocessing</h2>
+<p><strong>preprocess the fastq files</strong></p>
+<p>Important for the clustering analysis:</p>
+<ul>
+<li>subsample to have the same number of reads between male and female</li>
+</ul>
+<p>Important for the <span class="math inline">\(k\)</span>-mer counting</p>
+<ul>
+<li>split the fastq files into managable size files (<span class="math inline">\(10ˆ6\)</span> reads per files)</li>
+</ul>
+</section>
+<section id="k-mer-count" class="slide level2">
+<h2><span class="math inline">\(k\)</span>-mer count</h2>
+<p><a href="https://github.com/angelovangel/fastkmers">fastqkmer</a></p>
+<pre><code>fastkmers -k 12 file.fastq > file.csv</code></pre>
+<p>Run a <strong>sliding windows</strong> of size <span class="math inline">\(12\)</span> by step of <span class="math inline">\(1\)</span> along the reads counting all the occurrences of each <span class="math inline">\(k\)</span>-mers</p>
+<p>We have the letters: <span class="math inline">\(A,C,T,G\)</span> and <span class="math inline">\(N\)</span></p>
+<div style="text-align: center">
+<span class="math inline">\(244,140,625\)</span> possible <span class="math inline">\(k\)</span>-mers
+</div>
+<p>We split the fastq files into <span class="math inline">\(\sim\)</span> <span class="math inline">\(1400\)</span> subfiles of <span class="math inline">\(10^6\)</span> reads.</p>
+</section>
+<section id="merging-the-k-mers" class="slide level2">
+<h2>Merging the <span class="math inline">\(k\)</span>-mers</h2>
+<p><span class="math inline">\(\sim\)</span> <span class="math inline">\(1400\)</span> splits of <span class="math inline">\(10^6\)</span> reads <span class="math inline">\(\rightarrow\)</span> <span class="math inline">\(1400\)</span> csv files</p>
+<div class="columns">
+<div class="column" style="width:50%;">
+<ul>
+<li>large number of <span class="math inline">\(k\)</span>-mers</li>
+<li>Unordered</li>
+<li>not the same <span class="math inline">\(k\)</span>-mers a present in every files</li>
+</ul>
+<p><a href="https://gitbio.ens-lyon.fr/LBMC/Delattre/mergekmer">mergekmer</a> a small rust programme that build a <strong>sufix-tree</strong> of the <span class="math inline">\(k\)</span>-mer</p>
+</div><div class="column" style="width:50%;">
+<p><img data-src="./img/sufixtree_a.png"></p>
+</div>
+</div>
+</section>
+<section id="merging-the-k-mers-1" class="slide level2">
+<h2>Merging the <span class="math inline">\(k\)</span>-mers</h2>
+<p><a href="https://gitbio.ens-lyon.fr/LBMC/Delattre/mergekmer">mergekmer</a> a small rust programme that build a <strong>sufix-tree</strong> of the <span class="math inline">\(k\)</span>-mer</p>
+<div class="columns">
+<div class="column" style="width:50%;">
+<pre><code>merge fastkmers output
+
+Usage: mergekmer [OPTIONS] --output <OUTPUT>
+
+Options:
+ -c, --csv <CSV>... list of csv files
+ -o, --output <OUTPUT> merged csv file
+ -c, --collate collate csv file
+ -h, --help Print help
+ -V, --version Print version</code></pre>
+<p>Each leafs of the tree contains the number of <span class="math inline">\(k\)</span>-mers</p>
+<p>The tree traversal is easy to compute with a recursive function</p>
+<p><strong>we can merge the counts of a given sex for each specie</strong></p>
+</div><div class="column" style="width:50%;">
+<p><img data-src="./img/sufixtree_b.png"></p>
+</div>
+</div>
+</section>
+<section id="merging-the-k-mers-2" class="slide level2">
+<h2>Merging the <span class="math inline">\(k\)</span>-mers</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<pre><code>merge fastkmers output
+
+Usage: mergekmer [OPTIONS] --output <OUTPUT>
+
+Options:
+ -c, --csv <CSV>... list of csv files
+ -o, --output <OUTPUT> merged csv file
+ -c, --collate collate csv file
+ -h, --help Print help
+ -V, --version Print version</code></pre>
+<p>In the <code>--collate</code> version earch leave contain a list of the count of the <span class="math inline">\(k\)</span>-mers in the female or male of a specie</p>
+<p><strong>we can fuse the counts of the male and female for each specie</strong></p>
+</div><div class="column" style="width:50%;">
+<p><img data-src="./img/sufixtree_c.png"></p>
+</div>
+</div>
+</section>
+<section id="test-the-sexual-model" class="slide level2">
+<h2>Test the sexual model</h2>
+<p><strong>We have the following possible models</strong></p>
+<div class="columns">
+<div class="column" style="width:33%;">
+<ul>
+<li><span style="color:red;">X</span><span style="color:green;">Y</span> system</li>
+</ul>
+<p><img data-src="./img/model_XY.png"></p>
+</div><div class="column" style="width:33%;">
+<ul>
+<li><span style="color:red;">X</span>O system</li>
+</ul>
+<p><img data-src="./img/model_XO.png"></p>
+</div><div class="column" style="width:33%;">
+<ul>
+<li>OO system</li>
+</ul>
+<p><img data-src="./img/model_OO.png"></p>
+</div>
+</div>
+</section>
+<section id="test-the-sexual-model-1" class="slide level2">
+<h2>Test the sexual model</h2>
+<div class="columns">
+<div class="column" style="width:33%;">
+<ul>
+<li><span style="color:red;">X</span><span style="color:green;">Y</span> system</li>
+</ul>
+<p><img data-src="./img/clustering_XY_naive.png"></p>
+</div><div class="column" style="width:33%;">
+<ul>
+<li><span style="color:red;">X</span>O system</li>
+</ul>
+<p><img data-src="./img/clustering_XO_naive.png"></p>
+</div><div class="column" style="width:33%;">
+<ul>
+<li>OO system</li>
+</ul>
+<p><img data-src="./img/clustering_OO_naive.png"></p>
+</div>
+</div>
+<ul>
+<li>A cluster with mean male <span class="math inline">\(=\)</span> mean female</li>
+<li>A cluster above the diagonale</li>
+<li>A cluster below the diagonale</li>
+</ul>
+</section>
+<section id="test-the-sexual-model-2" class="slide level2">
+<h2>Test the sexual model</h2>
+<div class="columns">
+<div class="column" style="width:25%;">
+<p><strong>data</strong></p>
+<p><img data-src="./img/model_XY.png"></p>
+</div><div class="column" style="width:25%;">
+<p><strong>XY model</strong></p>
+<p><img data-src="./img/clustering_XY_naive_XY.png"></p>
+</div><div class="column" style="width:25%;">
+<p><strong>XO model</strong></p>
+<p><img data-src="./img/clustering_XY_naive_XO.png"></p>
+</div><div class="column" style="width:25%;">
+<p><strong>OO model</strong></p>
+<p><img data-src="./img/clustering_XY_naive_OO.png"></p>
+</div>
+</div>
+<div class="columns">
+<div class="column" style="width:50%;">
+<p>Bayesian information criterion (BIC)</p>
+<p><img data-src="./img/clustering_XY_naive_BIC.png"></p>
+</div><div class="column" style="width:50%;">
+<p>Loglikelihood</p>
+<p><img data-src="./img/clustering_XY_naive_loglik.png"></p>
+</div>
+</div>
+</section>
+<section id="identify-the-ax-and-y-k-mers" class="slide level2">
+<h2>identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> <span class="math inline">\(k\)</span>-mers</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<p><img data-src="./img/clustering_XY_naive_XY.png"></p>
+</div><div class="column" style="width:50%;">
+<ul>
+<li>Can be used to compare model</li>
+<li>Not sensitive enough</li>
+<li>Cannot be used to classify individual <span class="math inline">\(k\)</span>-mers</li>
+</ul>
+</div>
+</div>
+</section>
+<section id="identify-the-ax-and-y-k-mers-1" class="slide level2">
+<h2>identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> <span class="math inline">\(k\)</span>-mers</h2>
+<div class="columns">
+<div class="column" style="width:75%;">
+<p><img data-src="./img/clustering_XY_bayse_XY.png"></p>
+</div><div class="column" style="width:25%;">
+<ul>
+<li>Can choose the prior for each cluster (mean and shape)</li>
+<li>Can choose the prior for the proportion between <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span></li>
+<li>Can choose the weight of each prior compared to the data</li>
+</ul>
+</div>
+</div>
+</section>
+<section id="identify-the-ax-and-y-k-mers-2" class="slide level2">
+<h2>identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> <span class="math inline">\(k\)</span>-mers</h2>
+<div class="columns">
+<div class="column" style="width:75%;">
+<p><img data-src="./img/clustering_XY_bayse_XO.png"></p>
+</div><div class="column" style="width:25%;">
+<ul>
+<li>Can choose the prior for each cluster (mean and shape)</li>
+<li>Can choose the prior for the proportion between <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span></li>
+<li>Can choose the weight of each prior compared to the data</li>
+</ul>
+</div>
+</div>
+</section>
+<section id="identify-the-ax-and-y-k-mers-3" class="slide level2">
+<h2>identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> <span class="math inline">\(k\)</span>-mers</h2>
+<div class="columns">
+<div class="column" style="width:75%;">
+<p><img data-src="./img/clustering_XO_bayse_XO.png"></p>
+</div><div class="column" style="width:25%;">
+<ul>
+<li>Can choose the prior for each cluster (mean and shape)</li>
+<li>Can choose the prior for the proportion between <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span></li>
+<li>Can choose the weight of each prior compared to the data</li>
+</ul>
+</div>
+</div>
+</section>
+<section id="count-problem" class="slide level2">
+<h2>Count problem</h2>
+<div class="columns">
+<div class="column" style="width:75%;">
+<p><img data-src="./img/count_problem.png"></p>
+</div><div class="column" style="width:25%;">
+<ul>
+<li>The coverage is not the same between the male and the female</li>
+</ul>
+</div>
+</div>
+</section>
+<section id="kmer-diff-2" class="slide level2">
+<h2>Kmer-diff</h2>
+<p>A nextflow pipeline to analyse the <span class="math inline">\(k\)</span>-mer content of fastq files</p>
+<ol type="1">
+<li>preprocess the fastq files
+<ul>
+<li><strong>subsample to have the same number of reads between male and female</strong></li>
+</ul></li>
+<li>count the <span class="math inline">\(k\)</span>-mers of each file</li>
+<li>merge the counts to get a table of male and female <span class="math inline">\(k\)</span>-mers counts</li>
+<li>test the sexual models</li>
+<li>identify the <span style="color:blue;">A</span>,<span style="color:red;">X</span> and <span style="color:green;">Y</span> <span class="math inline">\(k\)</span>-mers</li>
+</ol>
+<div class="footer footer-default">
+<p>laurent.modolo@ens-lyon.fr</p>
+</div>
+</section>
+ </div>
+ </div>
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