Exercise and answers - Revision history

Mick at 08:09, 9 January 2026

2026-01-09T08:09:07Z

← Older revision		Revision as of 10:09, 9 January 2026
Line 3:		Line 3:
	<p>		<p>
	In this mini-workshop you will familiarize yourself with <b>TADbit</b>		In this mini-workshop you will familiarize yourself with <b>TADbit</b>
	(~~<a href="~~https://pubmed.ncbi.nlm.nih.gov/28723903/~~" target="_blank" rel="noopener">~~Serra et al., 2017~~</a>~~):		([https://pubmed.ncbi.nlm.nih.gov/28723903/ Serra et al., 2017]):
	from FASTQ files to contact matrix and beyond.		from FASTQ files to contact matrix and beyond.
	</p>		</p>
Line 324:		Line 324:

	<ul>		<ul>
	<li>~~<a href="~~https://teaching.healthtech.dtu.dk/material/22126/2026/Fragment_histogram.pdf~~" target="_blank" rel="noopener">~~Fragment size histogram ~~(PDF)</a>~~</li>		<li>[https://teaching.healthtech.dtu.dk/material/22126/2026/Fragment_histogram.pdf Fragment size histogram]</li>
	<li>~~<a href="~~https://teaching.healthtech.dtu.dk/material/22126/2026/ligation_deconvolution.png~~" target="_blank" rel="noopener">~~Hi-C sequencing quality: digestion/ligation deconvolution ~~(PNG)</a>~~</li>		<li>[https://teaching.healthtech.dtu.dk/material/22126/2026/ligation_deconvolution.png Hi-C sequencing quality: digestion/ligation deconvolution ]</li>
	</ul>		</ul>

Line 507:		Line 507:

	<p>		<p>
	~~<a href="~~https://www.tandfonline.com/doi/full/10.2144/btn-2019-0105~~" target="_blank" rel="noopener">~~		[https://www.tandfonline.com/doi/full/10.2144/btn-2019-0105 Overview article on Hi-C normalization strategies]
	Overview article on Hi-C normalization strategies
	~~</a>~~
	</p>		</p>

Line 557:		Line 555:

	<ul>		<ul>
	<li>~~<a href="~~https://teaching.healthtech.dtu.dk/material/22126/2026/Raw_HiC.png~~" target="_blank" rel="noopener">~~Raw Hi-C matrix ~~(PNG)</a>~~</li>		<li>[https://teaching.healthtech.dtu.dk/material/22126/2026/Raw_HiC.png Raw Hi-C matrix] </li>
	<li>~~<a href="~~https://teaching.healthtech.dtu.dk/material/22126/2026/Normal_HiC.png~~" target="_blank" rel="noopener">~~Normalized Hi-C matrix ~~(PNG)</a>~~</li>		<li>[https://teaching.healthtech.dtu.dk/material/22126/2026/Normal_HiC.png Normalized Hi-C matrix] </li>
	~~</ul~~>

	<p><b>Congratulations, you finished the exercise!</b></p>		<p><b>Congratulations, you finished the exercise!</b></p>

Mick at 08:02, 9 January 2026

2026-01-09T08:02:44Z

Show changes

Mick at 09:23, 8 January 2026

2026-01-08T09:23:36Z

← Older revision		Revision as of 11:23, 8 January 2026
Line 482:		Line 482:

	<hr>		<hr>

			<p>
			[https://teaching.healthtech.dtu.dk/material/22126/2026/Raw_HiC.png Raw HiC matrix]
			</p>
			<p>
			[https://teaching.healthtech.dtu.dk/material/22126/2026/Normal_HiC.png Normalized HiC matrix]
			</p>


	<p><b>Congratulations, you finished the exercise!</b></p>		<p><b>Congratulations, you finished the exercise!</b></p>

Mick at 09:18, 8 January 2026

2026-01-08T09:18:15Z

← Older revision		Revision as of 11:18, 8 January 2026
Line 288:		Line 288:

	<p><b>Question:</b> How may restriction enzyme choice influence the experiment? ✂️</p>		<p><b>Question:</b> How may restriction enzyme choice influence the experiment? ✂️</p>
	<p><b>Answer:</b> ~~How may restriction enzyme choice influence the experiment? ✂️~~		<p><b>Answer:</b> Cutting frequency differs between 4‑cutters and 6‑cutters and influences fragment size distribution, ligation probabilities, and contact resolution. Using two enzymes increases the diversity of ligation junctions. Compare with Micro‑C, which uses MNase digestion, so it cuts evenly through the genome.</p>
	Cutting frequency differs between 4‑cutters and 6‑cutters and influences fragment size distribution, ligation probabilities, and contact resolution. Using two enzymes increases the diversity of ligation junctions. Compare with Micro‑C, which uses MNase digestion, so it cuts evenly through the genome.</p>		[https://teaching.healthtech.dtu.dk/material/22126/2026/Fragment_histogram.pdf Fragment size histogram]
	([https://teaching.healthtech.dtu.dk/material/22126/2026/Fragment_histogram.pdf Fragment size histogram])		[https://teaching.healthtech.dtu.dk/material/22126/2026/ligation_deconvolution.png HiC Sequencing Quality and digestion - ligation deconvolution]
	([https://teaching.healthtech.dtu.dk/material/22126/2026/ligation_deconvolution.png HiC Sequencing Quality and digestion - ligation deconvolution])


Line 331:		Line 330:

	<p><b>Question:</b> Is it possible to retrieve multiple contacting regions?</p>		<p><b>Question:</b> Is it possible to retrieve multiple contacting regions?</p>
			<p><b>Answer:</b> Consider complex ligation products (read pairs mapping to different fragments in the same molecule, i.e., multiple contacts) and multi‑mapping artifacts; TADbit focuses on valid pairs as operationally defined by the filters. Multi‑contact methods (e.g., Pore‑C, SPRITE) address this explicitly, but standard Hi‑C largely models binary contacts per ligation event. We can view it on the bam file in the next step.</p>

	<hr>		<hr>
Line 368:		Line 368:

	<p><b>Question:</b> How many valid pairs do we keep?</p>		<p><b>Question:</b> How many valid pairs do we keep?</p>
			<p><b>Answer:</b>Check the “valid pairs” section of tadbit describe after filtering to get the exact count and percentage regarding the initial read pairs.</p>
	<p><b>Question:</b> The total number of filtered reads is not equal to the initial number of reads… Why?</p>		<p><b>Question:</b> The total number of filtered reads is not equal to the initial number of reads… Why?</p>
			<p><b>Answer:</b>Because a read pair can be assigned to more than one category (e.g., a dangling end that is also a duplicate). Categories are not mutually exclusive, so percentages can overlap.</p>

	<hr>		<hr>

Mick at 09:15, 8 January 2026

2026-01-08T09:15:52Z

← Older revision		Revision as of 11:15, 8 January 2026
Line 228:		Line 228:

	<p><b>Question:</b> Check the HTML report. What percentage of reads are kept?</p>		<p><b>Question:</b> Check the HTML report. What percentage of reads are kept?</p>

			<p><b>Answer:</b> It should be about ~96.4%. No massive adapter content or low quality sequences. After mapping we will inspect ligation/digestion patterns in more detail.</p>


	<hr>		<hr>
Line 285:		Line 288:

	<p><b>Question:</b> How may restriction enzyme choice influence the experiment? ✂️</p>		<p><b>Question:</b> How may restriction enzyme choice influence the experiment? ✂️</p>
			<p><b>Answer:</b> How may restriction enzyme choice influence the experiment? ✂️
			Cutting frequency differs between 4‑cutters and 6‑cutters and influences fragment size distribution, ligation probabilities, and contact resolution. Using two enzymes increases the diversity of ligation junctions. Compare with Micro‑C, which uses MNase digestion, so it cuts evenly through the genome.</p>
			([https://teaching.healthtech.dtu.dk/material/22126/2026/Fragment_histogram.pdf Fragment size histogram])
			([https://teaching.healthtech.dtu.dk/material/22126/2026/ligation_deconvolution.png HiC Sequencing Quality and digestion - ligation deconvolution])


	<ul>		<ul>

Mick at 10:17, 7 January 2026

2026-01-07T10:17:33Z

← Older revision		Revision as of 12:17, 7 January 2026
Line 33:		Line 33:
	<hr>		<hr>

	<h2>Setup conda environment to run TADbit later <b>You will get notified something is missing, just accept</b~~></h2~~>		<h2>Setup conda environment to run TADbit later</h2> <b>You will get notified something is missing, just accept</b>

	<pre>		<pre>

Mick at 10:17, 7 January 2026

2026-01-07T10:17:00Z

← Older revision		Revision as of 12:17, 7 January 2026
Line 33:		Line 33:
	<hr>		<hr>

	<h2>Setup conda environment to run TADbit later</h2>		<h2>Setup conda environment to run TADbit later <b>You will get notified something is missing, just accept</b></h2>

	<pre>		<pre>
	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>

Line 75:		Line 75:

	# 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: Created page with "

Overview

In this mini-workshop you will familiarize yourself with TADbit (Serra et al., 2017): from FASTQ files to contact matrix and beyond.

A Primer into 3D Genomics: A Mini-Workshop
Juan Antonio Rodríguez, Globe Institute, University of Copenhagen
9 January 2026, DTU

Outline of the exercises

Preprocess Hi-C FASTQ data
Index reference genome
Use TADbit to: