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<h1 class="title toc-ignore">index</h1>
<h4 class="author">Ruqian Lyu</h4>
<h4 class="date">11/28/2021</h4>
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<p>
<button type="button" class="btn btn-default btn-workflowr btn-workflowr-report" data-toggle="collapse" data-target="#workflowr-report">
<span class="glyphicon glyphicon-list" aria-hidden="true"></span> workflowr <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span>
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<a data-toggle="tab" href="#checks"> Checks <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> </a>
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<a data-toggle="tab" href="#versions">Past versions</a>
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<p>
<strong>Last updated:</strong> 2021-11-28
</p>
<p>
<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 7 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
</p>
<p>
<strong>Knit directory:</strong> <code>Hinch2019/analysis/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
</p>
<p>
This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a
href="https://github.com/jdblischak/workflowr">workflowr</a> (version 1.6.2). The <em>Checks</em> tab describes the reproducibility checks that were applied when the results were created. The <em>Past versions</em> tab lists the development history.
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguptodate"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>R Markdown file:</strong> up-to-date </a>
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<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongEnvironmentstrongempty"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Environment:</strong> empty </a>
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<div id="strongEnvironmentstrongempty" class="panel-collapse collapse">
<div class="panel-body">
<p>Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity itโs best to always run the code in an empty environment.</p>
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</div>
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<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongSeedstrongcodesetseed12345code"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Seed:</strong> <code>set.seed(12345)</code> </a>
</p>
</div>
<div id="strongSeedstrongcodesetseed12345code" class="panel-collapse collapse">
<div class="panel-body">
<p>The command <code>set.seed(12345)</code> was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongSessioninformationstrongrecorded"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Session information:</strong> recorded </a>
</p>
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<p>Great job! Recording the operating system, R version, and package versions is critical for reproducibility.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongCachestrongnone"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Cache:</strong> none </a>
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<div id="strongCachestrongnone" class="panel-collapse collapse">
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<p>Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongFilepathsstrongrelative"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>File paths:</strong> relative </a>
</p>
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<div id="strongFilepathsstrongrelative" class="panel-collapse collapse">
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<p>Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.</p>
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<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublichinchsinglespermDNAseqprocessingtreea5f11c9c9e71b4c9cdae10b3930a48a292825fe2targetblanka5f11c9a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-public/hinch-single-sperm-DNA-seq-processing/tree/a5f11c9c9e71b4c9cdae10b3930a48a292825fe2" target="_blank">a5f11c9</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublichinchsinglespermDNAseqprocessingtreea5f11c9c9e71b4c9cdae10b3930a48a292825fe2targetblanka5f11c9a" class="panel-collapse collapse">
<div class="panel-body">
<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/biocellgen-public/hinch-single-sperm-DNA-seq-processing/tree/a5f11c9c9e71b4c9cdae10b3930a48a292825fe2" target="_blank">a5f11c9</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
</p>
<pre><code>
Ignored files:
Ignored: .Rproj.user/
Ignored: code/
Untracked files:
Untracked: .gitignore
Untracked: .snakemake/
Untracked: Hinch2019.Rproj
Untracked: Snakefile_hinch.log.out
Untracked: SraRunTable_hinch.txt
Untracked: analysis/
Untracked: data/
Untracked: envs/
Untracked: fastp.html
Untracked: fastp.json
Untracked: output/
Untracked: references/
Untracked: sampleNames.txt
Untracked: srr_failed.txt
Untracked: submit-runAlign.sh
Untracked: submit-subsample.sh
Untracked: success.txt
Unstaged changes:
Modified: sampleNames_meta.txt
Modified: submit-mergeBams.sh
Modified: submit-runDenovoVC.sh
Modified: submit-wgetSRAFastqdump.sh
</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
</p>
</div>
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</div>
</div>
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<p>
There are no past versions. Publish this analysis with <code>wflow_publish()</code> to start tracking its development.
</p>
<hr>
</div>
</div>
</div>
<div id="introduction" class="section level2">
<h2>Introduction</h2>
<p>Application of <code>comapr</code> on public dataset</p>
<p>1 <a href="Crossover-identification-with-sscocaller-and-comapr.html">comapr application</a></p>
<br>
<p>
<button type="button" class="btn btn-default btn-workflowr btn-workflowr-sessioninfo" data-toggle="collapse" data-target="#workflowr-sessioninfo" style="display: block;">
<span class="glyphicon glyphicon-wrench" aria-hidden="true"></span> Session information
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<div id="workflowr-sessioninfo" class="collapse">
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code></pre></div>
<pre><code>R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.4 (Ootpa)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 knitr_1.36 magrittr_2.0.1 workflowr_1.6.2
[5] R6_2.5.1 rlang_0.4.11 fastmap_1.1.0 fansi_0.5.0
[9] stringr_1.4.0 tools_4.1.0 xfun_0.26 utf8_1.2.2
[13] jquerylib_0.1.4 git2r_0.28.0 htmltools_0.5.2 ellipsis_0.3.2
[17] rprojroot_2.0.2 yaml_2.2.1 digest_0.6.28 tibble_3.1.4
[21] lifecycle_1.0.1 crayon_1.4.1 later_1.3.0 vctrs_0.3.8
[25] promises_1.2.0.1 fs_1.5.0 glue_1.4.2 evaluate_0.14
[29] rmarkdown_2.11 stringi_1.7.4 compiler_4.1.0 pillar_1.6.3
[33] httpuv_1.6.3 pkgconfig_2.0.3 </code></pre>
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