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User Guide update for v0.17.0 release
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<nav id="TOC"><ul><li><a href="#bismark-bisulfite-mapper">Bismark Bisulfite Mapper</a><ul><li><a href="#user-guide-v">User Guide - v0.16.3</a></ul></li><li><a href="#quick-reference">1) Quick Reference</a><ul><li><a href="#i-running-bismark-genome-preparation">(I) Running <code>bismark_genome_preparation</code></a></li><li><a href="#ii-running-bismark">(II) Running <code>bismark</code></a></li><li><a href="#iii-running-bismark-methylation-extractor">(III) Running <code>bismark_methylation_extractor</code></a></li><li><a href="#iv-running-bismark-report">(IV) Running <code>bismark2report</code></a></li><li><a href="#v-running-bismark-summary">(V) Running <code>bismark2summary</code></a></ul></li><li><a href="#bismark-general-information">2) Bismark - General Information</a><ul><li><a href="#what-is-bismark">What is Bismark?</a></li><li><a href="#installation-notes">Installation notes</a></li><li><a href="#dependencies">Dependencies</a></li><li><a href="#hardware-requirements">Hardware requirements</a></li><li><a href="#bs-seq-test-data-set">BS-Seq test data set</a></li><li><a href="#which-kind-of-bs-seq-files-are-supported">Which kind of BS-Seq files are supported?</a></li><li><a href="#how-does-bismark-work">How does Bismark work?</a></li><li><a href="#bismark-alignment-and-methylation-call-report">Bismark alignment and methylation call report</a></ul></li><li><a href="#running-bismark">3) Running Bismark</a><ul><li><a href="#i-bismark-genome-preparation">(I) Bismark Genome Preparation</a></li><li><a href="#ii-bismark-alignment-step">(II) Bismark Alignment Step</a></li><li><a href="#iii-bismark-methylation-extractor">(III) Bismark methylation extractor</a></li><li><a href="#iv-the-bismark-html-processing-report">(IV) The Bismark HTML Processing Report</a></li><li><a href="#v-the-bismark-summary-report">(V) The Bismark Summary Report</a></li><li><a href="#vi-bismark-nucleotide-coverage-report-bam-nuc">(VI) Bismark Nucleotide Coverage report (<code>bam2nuc</code>)</a></li><li><a href="#vii-filtering-out-non-bisulfite-converted-reads-filter-non-conversion">(VII) Filtering out non-bisulfite converted reads (<code>filter_non_conversion</code>)</a></li><li><a href="#viii-notes-about-different-library-types-and-commercial-kits">(VIII) Notes about different library types and commercial kits</a></ul></li><li><a href="#appendix-full-list-of-options">4) APPENDIX - Full list of options</a><ul><li><a href="#appendix-i-bismark-genome-preparation">Appendix (I): Bismark Genome Preparation</a></li><li><a href="#appendix-ii-bismark">Appendix (II): Bismark</a></li><li><a href="#appendix-iii-bismark-methylation-extractor">Appendix (III): Bismark Methylation Extractor</a></li><li><a href="#appendix-iv-bismark-reports-for-the-test-data-set">Appendix (IV): Bismark reports for the test data set</a></ul></li><li><a href="#credits">Credits</a></li></ul></nav>
<nav id="TOC"><ul><li><a href="#bismark-bisulfite-mapper">Bismark Bisulfite Mapper</a><ul><li><a href="#user-guide-v">User Guide - v0.17.0</a></ul></li><li><a href="#quick-reference">1) Quick Reference</a><ul><li><a href="#i-running-bismark-genome-preparation">(I) Running <code>bismark_genome_preparation</code></a></li><li><a href="#ii-running-bismark">(II) Running <code>bismark</code></a></li><li><a href="#iii-running-bismark-methylation-extractor">(III) Running <code>bismark_methylation_extractor</code></a></li><li><a href="#iv-running-bismark-report">(IV) Running <code>bismark2report</code></a></li><li><a href="#v-running-bismark-summary">(V) Running <code>bismark2summary</code></a></ul></li><li><a href="#bismark-general-information">2) Bismark - General Information</a><ul><li><a href="#what-is-bismark">What is Bismark?</a></li><li><a href="#installation-notes">Installation notes</a></li><li><a href="#dependencies">Dependencies</a></li><li><a href="#hardware-requirements">Hardware requirements</a></li><li><a href="#bs-seq-test-data-set">BS-Seq test data set</a></li><li><a href="#which-kind-of-bs-seq-files-are-supported">Which kind of BS-Seq files are supported?</a></li><li><a href="#how-does-bismark-work">How does Bismark work?</a></li><li><a href="#bismark-alignment-and-methylation-call-report">Bismark alignment and methylation call report</a></ul></li><li><a href="#running-bismark">3) Running Bismark</a><ul><li><a href="#i-bismark-genome-preparation">(I) Bismark Genome Preparation</a></li><li><a href="#ii-bismark-alignment-step">(II) Bismark Alignment Step</a></li><li><a href="#iii-bismark-methylation-extractor">(III) Bismark methylation extractor</a></li><li><a href="#iv-the-bismark-html-processing-report">(IV) The Bismark HTML Processing Report</a></li><li><a href="#v-the-bismark-summary-report">(V) The Bismark Summary Report</a></li><li><a href="#vi-bismark-nucleotide-coverage-report-bam-nuc">(VI) Bismark Nucleotide Coverage report (<code>bam2nuc</code>)</a></li><li><a href="#vii-filtering-out-non-bisulfite-converted-reads-filter-non-conversion">(VII) Filtering out non-bisulfite converted reads (<code>filter_non_conversion</code>)</a></li><li><a href="#viii-notes-about-different-library-types-and-commercial-kits">(VIII) Notes about different library types and commercial kits</a></ul></li><li><a href="#appendix-full-list-of-options">4) APPENDIX - Full list of options</a><ul><li><a href="#appendix-i-bismark-genome-preparation">Appendix (I): Bismark Genome Preparation</a></li><li><a href="#appendix-ii-bismark">Appendix (II): Bismark</a></li><li><a href="#appendix-iii-bismark-methylation-extractor">Appendix (III): Bismark Methylation Extractor</a></li><li><a href="#appendix-iv-bismark-reports-for-the-test-data-set">Appendix (IV): Bismark reports for the test data set</a></ul></li><li><a href="#credits">Credits</a></li></ul></nav>
<h1 id="bismark-bisulfite-mapper">Bismark Bisulfite Mapper</h1>

<p><img title="Bismark" id="header_img" src="Images/bismark.png"></p>

<h2 id="user-guide-v">User Guide - v0.16.3</h2>
<h2 id="user-guide-v">User Guide - v0.17.0</h2>

<h4 id="december">14 December, 2016</h4>
<h4 id="january">18 January, 2017</h4>

<p>This User Guide outlines the Bismark suite of tools and gives more details for each individual step. For troubleshooting some of the more commonly experienced problems in sequencing in general and bisulfite-sequencing in particular please browse through the sequencing section at <a href="https://sequencing.qcfail.com/">QCFail.com</a>.</p>

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