Alignment exercise - Revision history

Mick at 09:47, 7 January 2026

2026-01-07T09:47:53Z

Mick at 09:29, 7 January 2026

2026-01-07T09:29:03Z

← Older revision		Revision as of 11:29, 7 January 2026
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	cd; # Home folder		cd; # Home folder
	cp /home/projects/22126_NGS/exercises/3D_GENOMICS_COURSE/SCRIPTS/setup_TADbit.sh .;		cp /home/projects/22126_NGS/exercises/3D_GENOMICS_COURSE/SCRIPTS/setup_TADbit.sh .;
	./setup_TADbit.sh		bash ./setup_TADbit.sh
	</pre>		</pre>

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	# Activate TADbit environment		# Activate TADbit environment
	~~conda activate~~ /home/~~people~~/$~~{USER}~~/envs/tadbit_course		eval "$(/home/ctools/miniconda3/bin/conda shell.bash hook)"
	~~# $USER is your user; it's an environment variable so no need to change it.~~		conda activate "$HOME/envs/tadbit_course"

	# Make a WORKING folder for the course		# Make a WORKING folder for the course

Mick at 09:22, 7 January 2026

2026-01-07T09:22:51Z

Show changes

Mick at 09:18, 7 January 2026

2026-01-07T09:18:43Z

← Older revision		Revision as of 11:18, 7 January 2026
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	cd; # Home directory		cd; # Home directory
	cp /home/projects/22126_NGS/exercises/3D_GENOMICS_COURSE/SCRIPTS/setup_TADbit.sh .		cp /home/projects/22126_NGS/exercises/3D_GENOMICS_COURSE/SCRIPTS/setup_TADbit.sh .
	./setup_TADbit.sh		bash ./setup_TADbit.sh
	</pre>		</pre>

Mick at 14:53, 6 January 2026

2026-01-06T14:53:03Z

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Mick at 10:15, 6 January 2026

2026-01-06T10:15:05Z

← Older revision		Revision as of 12:15, 6 January 2026
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	<pre>		<pre>
	scp stud0XX@pupilX:path/to/NA19201*.png .		scp stud0XX@pupilX.healthtech.dtu.dk:path/to/NA19201*.png .
	</pre>		</pre>

Mick at 10:15, 5 January 2026

2026-01-05T10:15:20Z

← Older revision		Revision as of 12:15, 5 January 2026
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	<p>We will use <code>mosdepth</code> to measure the average coverage (mean number of reads covering each base in the genome):</p>		<p>We will use <code>mosdepth</code> to measure the average coverage (mean number of reads covering each base in the genome):</p>
	<pre>mosdepth [output_prefix] [input.sorted.bam]</pre>		<pre>/home/ctools/mosdepth/mosdepth [output_prefix] [input.sorted.bam]</pre>

	<p>Use any prefix you like (e.g. <code>SRR8002634_1</code>). <code>mosdepth</code> will write a summary file named <code>[output_prefix].mosdepth.summary.txt</code>.</p>		<p>Use any prefix you like (e.g. <code>SRR8002634_1</code>). <code>mosdepth</code> will write a summary file named <code>[output_prefix].mosdepth.summary.txt</code>.</p>

Mick at 10:55, 19 December 2025

2025-12-19T10:55:29Z

← Older revision		Revision as of 12:55, 19 December 2025
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	<p><b>Viewing the BAM statistics report:</b></p>		<p><b>Viewing the BAM statistics report:</b></p>

	<p>The command above generates ~~an HTML report (~~<~~code~~>~~NA19201.html~~</~~code~~>).</p>		<p>The command above generates a set of <b>PNG image files</b> containing
			various BAM statistics (e.g. insert size, base composition, quality by cycle).
			The plots are created in the current directory.</p>

	<p>If you are using <b>MobaXterm</b>, you can open the ~~HTML file~~ directly from the		<p>If you are using <b>MobaXterm</b>, you can open the PNG files directly from the
	left-hand file panel.</p>		left-hand file panel.</p>

	<p>If you are using <b>macOS</b> (or a standard terminal), copy the ~~HTML file~~ to your		<p>If you are using <b>macOS</b> (or a standard terminal), copy the PNG files to your
	local computer and open ~~it in a web browser~~. For example:</p>		local computer and open them using any image viewer. For example:</p>

	<pre>		<pre>
	scp stud0XX@pupilX:path/to/NA19201.~~html~~ .		scp stud0XX@pupilX:path/to/NA19201*.png .
	</pre>		</pre>

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	compute node you are working on.</p>		compute node you are working on.</p>

			<p><b>Q19:</b> Look at the <b>insert size distribution</b> plot. What is the most
	<p><b>Q19:</b> Look at the insert size distribution plot. What is the most common insert size (approximately)?</p>		common insert size (approximately)?</p>

	<hr>		<hr>

Mick at 14:22, 16 December 2025

2025-12-16T14:22:59Z

@@ Line 324: / Line 324: @@
 <h4>stat</h4>
-<p>Generate additional statistics using:</p>
+<p>Generate additional alignment statistics using:</p>
-<p>Redirect the output to a file (e.g. <code>NA19201.stat</code>).</p>
+<pre>
 <p><b>Q19:</b> Look at the insert size distribution plot. What is the most common insert size (approximately)?</p>

Mick at 12:18, 11 December 2025

2025-12-11T12:18:27Z

← Older revision		Revision as of 14:18, 11 December 2025
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	<hr>		<hr>

	<h3>Inspecting the alignment ~~in IGV~~</h3>		<h3>Inspecting the alignment with <code>samtools tview</code></h3>

	<p>We will use ~~IGV (Integrative Genomics Viewer)~~ to inspect the human alignment.</p>		<p>We will use the text-based viewer <code>samtools tview</code> to inspect the human alignment around a potential variant.</p>

	<p>~~Start IGV~~:</p>		<p>First, make sure your BAM file is indexed:</p>
	<pre>~~igv &~~</pre>		<pre>samtools index NA19201.bam</pre>

	<p>Then:</p>		<p>Then start <code>samtools tview</code>:</p>
			<pre>samtools tview NA19201.bam /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa</pre>

			<p>This opens the alignment in your terminal.</p>

			<p>To jump to the region of interest (<code>chr20:35,581,362</code>):</p>
	<ol>		<ol>
	<li>~~In the genome dropdown, choose “More…”, then select <b>Human hg38</b> and click OK.</li>~~		<li>Press <code>g</code> (for “goto”).</li>
	~~<li>Go to “File” → “Load from File…” and select your~~ <code>~~NA19201.bam~~</code> ~~file~~.</li>		<li>Type <code>chr20:35581362</code> and press Enter.</li>
	<li>~~In the chromosome dropdown, select <code>chr20</code>.</li>~~
	~~<li>In the coordinate box, enter:~~ <code>chr20:~~35,581,362~~</code> and press Enter.</li>
	</ol>		</ol>

	<p>~~There appears to be a variant at this position~~. ~~Use IGV to answer~~:</p>		<p>You should now see:</p>
			<ul>
			<li>The reference sequence on the top line.</li>
			<li>Aligned reads below. Matching bases are often shown as <code>.</code> or <code>,</code>, while mismatches are shown as the actual base (A/C/G/T).</li>
			</ul>

			<p>Useful keys:</p>
			<ul>
			<li><code>?</code> – show help.</li>
			<li>Arrow keys – move left/right/up/down.</li>
			<li><code>q</code> – quit <code>tview</code>.</li>
			</ul>

	<p>~~<b>Q20:</b> What is the reference base at~~ this ~~position? What base is present in~~ the ~~sample reads?~~</p>		<p>Use this view to answer the following:</p>

	<p><b>~~Q21~~:</b> ~~How many~~ reads ~~support the non-reference base~~?</p>		<p><b>Q20:</b> At position <code>chr20:35,581,362</code>, what bases are present in the sample reads?</p>

	<p><b>~~Q22~~:</b> ~~This variant lies within a gene. What is~~ the ~~name of~~ the ~~gene?~~</p>		<p><b>Q21:</b> How many reads support the non-consensus base at this position? (Count the reads showing the alternative base in <code>tview</code>.)</p>

	<p>~~Feel free to explore other regions~~ on ~~chromosome 20 using IGV~~.</p>		<p><b>Q22:</b> Based on the fraction of reads supporting the non-reference base, does this variant look more like a heterozygous or a homozygous variant? Explain briefly.</p>

	<hr>		<hr>