From 39cec4017cef73330981cecfd4ab589e8210e74f Mon Sep 17 00:00:00 2001
From: arq5x <arq5x@virginia.edu>
Date: Thu, 20 Nov 2014 09:42:46 -0500
Subject: [PATCH] better tutorial
---
tutorial/answers.html | 8 +++--
tutorial/answers.md | 8 +++--
tutorial/bedtools.html | 43 ++++++++++++++++++++++--
tutorial/bedtools.md | 2 +-
tutorial/template.html | 75 ++++++++++++++++++++++++++++++++++++++++++
5 files changed, 129 insertions(+), 7 deletions(-)
create mode 100644 tutorial/template.html
diff --git a/tutorial/answers.html b/tutorial/answers.html
index 769de7c7..81ee0d88 100644
--- a/tutorial/answers.html
+++ b/tutorial/answers.html
@@ -25,10 +25,14 @@
<div class="span12">
<h1 id="puzzles-to-help-teach-you-more-bedtools.">Puzzles to help teach you more bedtools.</h1>
<ol style="list-style-type: decimal">
-<li>Create a BED file representing all of the intervals in the genome that are NOT exonic.</li>
+<li>Create a BED file representing all of the intervals in the genome that are NOT exonic and are not Promoters (based on the promoters in the hESC file).</li>
</ol>
<p>Answer:</p>
-<pre><code>bedtools complement -i exons.bed -g genome.txt > notexons.bed</code></pre>
+<pre><code>grep Promoter hesc.chromHmm.bed > hesc.promoters.bed
+
+cat exons.bed hesc.promoters.bed | sort -k1,1 -k2,2n | exons.and.promoters.bed
+
+bedtools complement -i exons.and.promoters.bed -g genome.txt > notexonsorpromoters.bed</code></pre>
<ol start="2" style="list-style-type: decimal">
<li>What is the average distance from GWAS SNPs to the closest exon? (Hint - have a look at the <a href="http://bedtools.readthedocs.org/en/latest/content/tools/closest.html">closest</a> tool.)</li>
</ol>
diff --git a/tutorial/answers.md b/tutorial/answers.md
index 95ef89cb..35cffe1c 100644
--- a/tutorial/answers.md
+++ b/tutorial/answers.md
@@ -6,11 +6,15 @@ Puzzles to help teach you more bedtools.
========================================
1. Create a BED file representing all of the intervals in the genome
-that are NOT exonic.
+that are NOT exonic and are not Promoters (based on the promoters in the hESC file).
Answer:
+
+ grep Promoter hesc.chromHmm.bed > hesc.promoters.bed
+
+ cat exons.bed hesc.promoters.bed | sort -k1,1 -k2,2n | exons.and.promoters.bed
- bedtools complement -i exons.bed -g genome.txt > notexons.bed
+ bedtools complement -i exons.and.promoters.bed -g genome.txt > notexonsorpromoters.bed
2. What is the average distance from GWAS SNPs to the closest exon? (Hint - have a look at the [closest](http://bedtools.readthedocs.org/en/latest/content/tools/closest.html) tool.)
diff --git a/tutorial/bedtools.html b/tutorial/bedtools.html
index 0f32657b..a4d4b8b8 100644
--- a/tutorial/bedtools.html
+++ b/tutorial/bedtools.html
@@ -22,7 +22,46 @@
</div>
<div class="container">
<div class="row">
- <div class="span12">
+ <div id="TOC" class="span3">
+ <div class="well toc">
+ <ul>
+ <li class="nav-header">Table of Contents</li>
+ </ul>
+ <ul>
+ <li><a href="#synopsis">Synopsis</a></li>
+ <li><a href="#setup">Setup</a></li>
+ <li><a href="#what-are-these-files">What are these files?</a></li>
+ <li><a href="#the-bedtools-help">The bedtools help</a></li>
+ <li><a href="#bedtools-intersect">bedtools “intersectâ€</a><ul>
+ <li><a href="#default-behavior">Default behavior</a></li>
+ <li><a href="#reporting-the-original-feature-in-each-file.">Reporting the original feature in each file.</a></li>
+ <li><a href="#how-many-base-pairs-of-overlap-were-there">How many base pairs of overlap were there?</a></li>
+ <li><a href="#counting-the-number-of-overlapping-features.">Counting the number of overlapping features.</a></li>
+ <li><a href="#find-features-that-do-not-overlap">Find features that DO NOT overlap</a></li>
+ <li><a href="#require-a-minimal-fraction-of-overlap.">Require a minimal fraction of overlap.</a></li>
+ <li><a href="#faster-analysis-via-sorted-data.">Faster analysis via sorted data.</a></li>
+ <li><a href="#intersecting-multiple-files-at-once.">Intersecting multiple files at once.</a></li>
+ </ul></li>
+ <li><a href="#bedtools-merge">bedtools “mergeâ€</a><ul>
+ <li><a href="#input-must-be-sorted">Input must be sorted</a></li>
+ <li><a href="#merge-intervals.">Merge intervals.</a></li>
+ <li><a href="#count-the-number-of-overlapping-intervals.">Count the number of overlapping intervals.</a></li>
+ <li><a href="#merging-features-that-are-close-to-one-another.">Merging features that are close to one another.</a></li>
+ <li><a href="#listing-the-name-of-each-of-the-exons-that-were-merged.">Listing the name of each of the exons that were merged.</a></li>
+ </ul></li>
+ <li><a href="#bedtools-complement">bedtools “complementâ€</a></li>
+ <li><a href="#bedtools-genomecov">bedtools “genomecovâ€</a><ul>
+ <li><a href="#producing-bedgraph-output">Producing BEDGRAPH output</a></li>
+ </ul></li>
+ <li><a href="#sophistication-through-chaining-multiple-bedtools">Sophistication through chaining multiple bedtools</a></li>
+ <li><a href="#principal-component-analysis">Principal component analysis</a><ul>
+ <li><a href="#a-jaccard-statistic-for-all-400-pairwise-comparisons.">A Jaccard statistic for all 400 pairwise comparisons.</a></li>
+ </ul></li>
+ <li><a href="#puzzles-to-help-teach-you-more-bedtools.">Puzzles to help teach you more bedtools.</a></li>
+ </ul>
+ </div>
+ </div>
+ <div class="span9">
<h1 id="synopsis">Synopsis</h1>
<p>Our goal is to work through examples that demonstrate how to explore, process and manipulate genomic interval files (e.g., BED, VCF, BAM) with the <code>bedtools</code> software package.</p>
<p>Some of our analysis will be based upon the Maurano et al exploration of DnaseI hypersensitivity sites in hundreds of primary tissue types.</p>
@@ -523,7 +562,7 @@ heatmap.2(jaccard_matrix, col = brewer.pal(9,"Blues"), margins = c(14,
<p><br /></p>
<h1 id="puzzles-to-help-teach-you-more-bedtools.">Puzzles to help teach you more bedtools.</h1>
<ol style="list-style-type: decimal">
-<li><p>Create a BED file representing all of the intervals in the genome that are NOT exonic.</p></li>
+<li><p>Create a BED file representing all of the intervals in the genome that are NOT exonic and not Promoters (based on the promoters in the hESC file).</p></li>
<li><p>What is the average distance from GWAS SNPs to the closest exon? (Hint - have a look at the <a href="http://bedtools.readthedocs.org/en/latest/content/tools/closest.html">closest</a> tool.)</p></li>
<li><p>Count how many exons occur in each 500kb interval (“windowâ€) in the human genome. (Hint - have a look at the <code>makewindows</code> tool.)</p></li>
<li><p>Are there any exons that are completely overlapped by an enhancer? If so, how many?</p></li>
diff --git a/tutorial/bedtools.md b/tutorial/bedtools.md
index 985afcf7..56bf2678 100644
--- a/tutorial/bedtools.md
+++ b/tutorial/bedtools.md
@@ -691,7 +691,7 @@ Puzzles to help teach you more bedtools.
1. Create a BED file representing all of the intervals in the genome
-that are NOT exonic.
+that are NOT exonic and not Promoters (based on the promoters in the hESC file).
2. What is the average distance from GWAS SNPs to the closest exon? (Hint - have a look at the [closest](http://bedtools.readthedocs.org/en/latest/content/tools/closest.html) tool.)
diff --git a/tutorial/template.html b/tutorial/template.html
new file mode 100644
index 00000000..8d2f7194
--- /dev/null
+++ b/tutorial/template.html
@@ -0,0 +1,75 @@
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--
GitLab