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pandoc --css bootstrap.css --template template.class.html -s -S bedtools.md -o bedtools.html
pandoc --css bootstrap.css --template template.class.html -s -S answers.md -o answers.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
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<meta http-equiv="Content-Style-Type" content="text/css" />
<meta name="generator" content="pandoc" />
<meta name="author" content="Aaron Quinlan" />
<title>bedtools Tutorial</title>
<style type="text/css">code{white-space: pre;}</style>
<link rel="stylesheet" href="bootstrap.css" type="text/css" />
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<body>
<div class="navbar navbar-static-top">
<div class="navbar-inner">
<div class="container">
<span class="doc-title">bedtools Tutorial</span>
<ul class="nav pull-right doc-info">
<li><p class="navbar-text">Aaron Quinlan</p></li>
</ul>
</div>
</div>
</div>
<div class="container">
<div class="row">
<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>
</ol>
<p>Answer:</p>
<pre><code>bedtools complement -i exons.bed -g genome.txt &gt; notexons.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>
<p>Answer:</p>
<pre><code>bedtools closest -a gwas.bed -b exons.bed -d | head
chr1 1005805 1005806 rs3934834 chr1 1007125 1007955 NM_001205252_exon_0_0_chr1_1007126_r 0 - 1320
chr1 1079197 1079198 rs11260603 chr1 1078118 1079434 NR_038869_exon_2_0_chr1_1078119_f 0 + 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_001256456_exon_1_0_chr1_1247398_r 0 - 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_001256460_exon_1_0_chr1_1247398_r 0 - 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_001256462_exon_1_0_chr1_1247398_r 0 - 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_001256463_exon_1_0_chr1_1247398_r 0 - 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_017871_exon_1_0_chr1_1247398_r 0 - 0
chr1 2069171 2069172 rs425277 chr1 2066700 2066786 NM_001033581_exon_1_0_chr1_2066701_f 0 + 2386
chr1 2069171 2069172 rs425277 chr1 2066700 2066786 NM_001033582_exon_1_0_chr1_2066701_f 0 + 2386
chr1 2069171 2069172 rs425277 chr1 2066700 2066786 NM_001242874_exon_1_0_chr1_2066701_f 0 + 2386
bedtools closest -a gwas.bed -b exons.bed -d \
| awk &#39;{ sum += $11 } END { if (NR &gt; 0) print sum / NR }&#39;
46713.1</code></pre>
<ol start="3" style="list-style-type: decimal">
<li>Count how many exons occur in each 500kb interval (“window”) in the human genome. (Hint - have a look at the <code>makewindows</code> tool.)</li>
</ol>
<p>Answer:</p>
<pre><code>bedtools makewindows -g genome.txt -w 500000 &gt; genome.windows.bed
bedtools intersect -a genome.windows.bed -b exons.bed -c &gt; genome.windows.exoncount.bedg</code></pre>
<p>or…</p>
<pre><code>bedtools makewindows -g genome.txt -w 500000 \
| bedtools intersect -a - -b exons.bed -c \
&gt; genome.windows.exoncount.bedg</code></pre>
<ol start="4" style="list-style-type: decimal">
<li>Are there any exons that are completely overlapped by an enhancer? If so, how many?</li>
</ol>
<p>Answer:</p>
<pre><code>bedtools intersect -a exons.bed \
-b &lt;(grep Enhancer hesc.chromHmm.bed) \
-wa -wb -f 1.0 \
| head
chr1 948846 948956 NM_005101_exon_0_0_chr1_948847_f 0 + chr1 948337 949337 4_Strong_Enhancer
chr1 1051439 1051736 NM_017891_exon_9_0_chr1_1051440_r 0 - chr1 1051337 1051737 6_Weak_Enhancer
chr1 1109285 1109306 NM_001130045_exon_0_0_chr1_1109286_f 0 + chr1 1108537 1109537 6_Weak_Enhancer
chr1 1109803 1109869 NM_001130045_exon_2_0_chr1_1109804_f 0 + chr1 1109737 1109937 6_Weak_Enhancer
chr1 1219357 1219470 NM_001130413_exon_4_0_chr1_1219358_f 0 + chr1 1219137 1220137 7_Weak_Enhancer
chr1 1219357 1219470 NR_037668_exon_4_0_chr1_1219358_f 0 + chr1 1219137 1220137 7_Weak_Enhancer
chr1 1229202 1229313 NM_030649_exon_1_0_chr1_1229203_r 0 - chr1 1228937 1229937 6_Weak_Enhancer
chr1 1229469 1229579 NM_030649_exon_2_0_chr1_1229470_r 0 - chr1 1228937 1229937 6_Weak_Enhancer
chr1 1234724 1234736 NM_030649_exon_14_0_chr1_1234725_r 0 - chr1 1234137 1234937 7_Weak_Enhancer
chr1 1245060 1245231 NM_153339_exon_4_0_chr1_1245061_f 0 + chr1 1244937 1245337 4_Strong_Enhancer
bedtools intersect -a exons.bed \
-b &lt;(grep Enhancer hesc.chromHmm.bed) \
-wa -wb -f 1.0 -u \
| wc -l
13746</code></pre>
<ol start="5" style="list-style-type: decimal">
<li>What fraction of the GWAS SNPs are exonic?</li>
</ol>
<p>Answer:</p>
<pre><code>wc -l gwas.bed
17680 gwas.bed
bedtools intersect -a gwas.bed -b exons.bed -u | wc -l
1625
echo &quot;foo&quot; | awk &#39;{print 1625/17680}&#39;
0.0919118</code></pre>
<ol start="6" style="list-style-type: decimal">
<li>What fraction of the GWAS SNPs are lie in either enhancers or promoters in the hESC data we have?</li>
</ol>
<p>Answer:</p>
<pre><code>bedtools intersect -a gwas.bed -b &lt;(egrep &quot;Enhancer|Promoter&quot; hesc.chromHmm.bed) -u \
| wc -l
1285
echo &quot;foo&quot; | awk &#39;{print 1285/17680}&#39;
0.072681</code></pre>
<ol start="7" style="list-style-type: decimal">
<li>Create intervals representing the canonical 2bp splice sites on either side of each exon (don’t worry about excluding splice sites at the first or last exon). (Hint - have a look at the <a href="http://bedtools.readthedocs.org/en/latest/content/tools/flank.html">flank</a> tool.)</li>
</ol>
<p>Answer:</p>
<pre><code>bedtools flank -l 2 -r 2 -i exons.bed -g genome.txt &gt; splice-sites.bed</code></pre>
<p>Or:</p>
<pre><code>bedtools slop -b 2 -i exons.bed -g genome.txt &gt; exons.plus2.bed
bedtools subtract -a exons.plus2.bed -b exons.bed &gt; splice-sites.bed</code></pre>
<ol start="8" style="list-style-type: decimal">
<li>What is the Jaccard statistic between CpG and hESC enhancers? Compare that to the Jaccard statistic between CpG and hESC promoters. Does the result make sense? (Hint - you will need <code>grep</code>).</li>
</ol>
<p>Answer:</p>
<pre><code>bedtools jaccard -a cpg.bed -b &lt;(grep Enhancer hesc.chromHmm.bed)
intersection union-intersection jaccard n_intersections
1148180 132977386 0.0086344 4969
bedtools jaccard -a cpg.bed -b &lt;(grep Promoter hesc.chromHmm.bed)
intersection union-intersection jaccard n_intersections
15661111 53551816 0.292448 20402</code></pre>
<ol start="9" style="list-style-type: decimal">
<li>What would you expect the Jaccard statistic to look like if promoters were randomly distributed throughout the genome? (Hint - you will need the <a href="http://bedtools.readthedocs.org/en/latest/content/tools/shuffle.html">shuffle</a> tool.)</li>
</ol>
<p>Answer:</p>
<pre><code>bedtools shuffle -i &lt;(grep Promoter hesc.chromHmm.bed) -g genome.txt \
| sort -k1,1 -k2,2n \
&gt; promoters.shuffled.bed
bedtools jaccard -a cpg.bed -b promoters.shuffled.bed
intersection union-intersection jaccard n_intersections
294071 68556207 0.00428949 78</code></pre>
<ol start="10" style="list-style-type: decimal">
<li>Which hESC ChromHMM state (e.g., 11_Weak_Txn, 10_Txn_Elongation) represents the most number of base pairs in the genome? (Hint: you will need to use <code>awk</code> or <code>perl</code> here, as well as the <a href="http://bedtools.readthedocs.org/en/latest/content/tools/groupby.html">groupby</a> tool.)</li>
</ol>
</div>
</div>
</div>
</body>
</html>
tutorial/answers.md 0 → 100644
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% bedtools Tutorial
% Aaron Quinlan
Puzzles to help teach you more bedtools.
========================================
1. Create a BED file representing all of the intervals in the genome
that are NOT exonic.
Answer:
bedtools complement -i exons.bed -g genome.txt > notexons.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.)
Answer:
bedtools closest -a gwas.bed -b exons.bed -d | head
chr1 1005805 1005806 rs3934834 chr1 1007125 1007955 NM_001205252_exon_0_0_chr1_1007126_r 0 - 1320
chr1 1079197 1079198 rs11260603 chr1 1078118 1079434 NR_038869_exon_2_0_chr1_1078119_f 0 + 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_001256456_exon_1_0_chr1_1247398_r 0 - 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_001256460_exon_1_0_chr1_1247398_r 0 - 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_001256462_exon_1_0_chr1_1247398_r 0 - 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_001256463_exon_1_0_chr1_1247398_r 0 - 0
chr1 1247493 1247494 rs12103 chr1 1247397 1247527 NM_017871_exon_1_0_chr1_1247398_r 0 - 0
chr1 2069171 2069172 rs425277 chr1 2066700 2066786 NM_001033581_exon_1_0_chr1_2066701_f 0 + 2386
chr1 2069171 2069172 rs425277 chr1 2066700 2066786 NM_001033582_exon_1_0_chr1_2066701_f 0 + 2386
chr1 2069171 2069172 rs425277 chr1 2066700 2066786 NM_001242874_exon_1_0_chr1_2066701_f 0 + 2386
bedtools closest -a gwas.bed -b exons.bed -d \
| awk '{ sum += $11 } END { if (NR > 0) print sum / NR }'
46713.1
3. Count how many exons occur in each 500kb interval ("window") in the human genome. (Hint - have a look at the `makewindows` tool.)
Answer:
bedtools makewindows -g genome.txt -w 500000 > genome.windows.bed
bedtools intersect -a genome.windows.bed -b exons.bed -c > genome.windows.exoncount.bedg
or...
bedtools makewindows -g genome.txt -w 500000 \
| bedtools intersect -a - -b exons.bed -c \
> genome.windows.exoncount.bedg
4. Are there any exons that are completely overlapped by an enhancer? If so, how many?
Answer:
bedtools intersect -a exons.bed \
-b <(grep Enhancer hesc.chromHmm.bed) \
-wa -wb -f 1.0 \
| head
chr1 948846 948956 NM_005101_exon_0_0_chr1_948847_f 0 + chr1 948337 949337 4_Strong_Enhancer
chr1 1051439 1051736 NM_017891_exon_9_0_chr1_1051440_r 0 - chr1 1051337 1051737 6_Weak_Enhancer
chr1 1109285 1109306 NM_001130045_exon_0_0_chr1_1109286_f 0 + chr1 1108537 1109537 6_Weak_Enhancer
chr1 1109803 1109869 NM_001130045_exon_2_0_chr1_1109804_f 0 + chr1 1109737 1109937 6_Weak_Enhancer
chr1 1219357 1219470 NM_001130413_exon_4_0_chr1_1219358_f 0 + chr1 1219137 1220137 7_Weak_Enhancer
chr1 1219357 1219470 NR_037668_exon_4_0_chr1_1219358_f 0 + chr1 1219137 1220137 7_Weak_Enhancer
chr1 1229202 1229313 NM_030649_exon_1_0_chr1_1229203_r 0 - chr1 1228937 1229937 6_Weak_Enhancer
chr1 1229469 1229579 NM_030649_exon_2_0_chr1_1229470_r 0 - chr1 1228937 1229937 6_Weak_Enhancer
chr1 1234724 1234736 NM_030649_exon_14_0_chr1_1234725_r 0 - chr1 1234137 1234937 7_Weak_Enhancer
chr1 1245060 1245231 NM_153339_exon_4_0_chr1_1245061_f 0 + chr1 1244937 1245337 4_Strong_Enhancer
bedtools intersect -a exons.bed \
-b <(grep Enhancer hesc.chromHmm.bed) \
-wa -wb -f 1.0 -u \
| wc -l
13746
5. What fraction of the GWAS SNPs are exonic?
Answer:
wc -l gwas.bed
17680 gwas.bed
bedtools intersect -a gwas.bed -b exons.bed -u | wc -l
1625
echo "foo" | awk '{print 1625/17680}'
0.0919118
6. What fraction of the GWAS SNPs are lie in either enhancers or promoters in the hESC data we have?
Answer:
bedtools intersect -a gwas.bed -b <(egrep "Enhancer|Promoter" hesc.chromHmm.bed) -u \
| wc -l
1285
echo "foo" | awk '{print 1285/17680}'
0.072681
7. Create intervals representing the canonical 2bp splice sites on either side of each exon (don't worry about excluding splice sites at the first or last exon). (Hint - have a look at the [flank](http://bedtools.readthedocs.org/en/latest/content/tools/flank.html) tool.)
Answer:
bedtools flank -l 2 -r 2 -i exons.bed -g genome.txt > splice-sites.bed
Or:
bedtools slop -b 2 -i exons.bed -g genome.txt > exons.plus2.bed
bedtools subtract -a exons.plus2.bed -b exons.bed > splice-sites.bed
8. What is the Jaccard statistic between CpG and hESC enhancers? Compare that to the Jaccard statistic between CpG and hESC promoters. Does the result make sense? (Hint - you will need `grep`).
Answer:
bedtools jaccard -a cpg.bed -b <(grep Enhancer hesc.chromHmm.bed)
intersection union-intersection jaccard n_intersections
1148180 132977386 0.0086344 4969
bedtools jaccard -a cpg.bed -b <(grep Promoter hesc.chromHmm.bed)
intersection union-intersection jaccard n_intersections
15661111 53551816 0.292448 20402
9. What would you expect the Jaccard statistic to look like if promoters were randomly distributed throughout the genome? (Hint - you will need the [shuffle](http://bedtools.readthedocs.org/en/latest/content/tools/shuffle.html) tool.)
Answer:
bedtools shuffle -i <(grep Promoter hesc.chromHmm.bed) -g genome.txt \
| sort -k1,1 -k2,2n \
> promoters.shuffled.bed
bedtools jaccard -a cpg.bed -b promoters.shuffled.bed
intersection union-intersection jaccard n_intersections
294071 68556207 0.00428949 78
10. Which hESC ChromHMM state (e.g., 11_Weak_Txn, 10_Txn_Elongation) represents the most number of base pairs in the genome? (Hint: you will need to use `awk` or `perl` here, as well as the [groupby](http://bedtools.readthedocs.org/en/latest/content/tools/groupby.html) tool.)
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