This exercise uses the dataset from the Nature publication by Ross-Inness et al., 2012. The goal of this article was to identify the binding sites of the Estrogen receptor, a transcription factor known to be associated with different types of breast cancer.

To this end, ChIP-seq was performed in breast cancer cells from 4 patients of different outcomes (good and poor). For each ChIP-seq experiment there is a matching technical control, i.e. there are 8 samples in total:

Half of which are the so-called ‘input’ samples for which the same treatment as the ChIP-seq samples was done except for the immunoprecipitation step. The input files are used to identify potential sequencing bias, like open chromatin or GC bias.

Because of the long processing time for the large original files, we have downsampled the original data and provide already processed data for subsequent steps.

Agenda

1. Step 1: Quality control and treatment of the sequences
2. Step 2: Mapping of the reads
   1. Visualization using a Genome Browser
   2. Inspection of the SAM format
3. Step 3: ChIP-seq Quality Control
   1. Correlation between samples
   2. IP strength estimation
4. Step 4: Normalization
   1. Generation of coverage files normalized by sequencing depth
   2. Generation of input-normalized coverage files and their visualization
5. Step 5: Detecting enriched regions (peak calling)
6. Step 6: Plot the signal on the peaks between samples
   1. computeMatrix
   2. plotHeatmap
7. Conclusion
8. Additional exercise (if you have finished all above)
   1. Additional Quality control : GC bias assessment
   2. Plotting heatmap from multiple samples with clustering

Step 1: Quality control and treatment of the sequences

The first step of any ChIP-Seq data analysis is quality control of the raw sequencing data.

Hands-on: Quality control

1. Create a new history for this tutorial and give it a proper name

   Tip: Creating a new history

   To create a new history simply click the new-history icon at the top of the history panel:

   

2. Import patient1_input_good_outcome from Zenodo or from the data library into the history

   Tip: Importing data via links

   • Copy the link location
   • Open the Galaxy Upload Manager
   • Select Paste/Fetch Data
   • Paste the link into the text field
   • Press Start and Close the window
   • Click on the pencil icon once the file is imported
   • Click on Datatype in the central panel
   • Select fastqsanger as New Type

   Tip: Importing data from a data library

   • Go into “Data” (top panel) then “Data libraries”
   • Click on “Training data” and then “Analyses of ChIP-Seq data”
   • Select interesting file
   • Click on “Import selected datasets into history”
   • Import in the history

   As default, Galaxy takes the link as name, so rename them.

3. Inspect the file by clicking on the eye icon

   Question

   1. How are the DNA sequences stored?
   2. What are the other entries?

   Solution

   1. The DNA sequences are stored in the second line of every 4-line group
   2. This file is called a FastQ file. It stores sequence information and quality information. Each sequence is represented by a group of 4 lines with the 1st line being the sequence id, the second the sequence of nucleotides, the third a transition line and the last one a sequence of quality score for each nucleotide.

4. Run FastQC tool with

   • “Short read data from your current history” to the imported file

   Inspect the generated files

It is often necessary to trim sequenced read, for example, to get rid of bases that were sequenced with high uncertainty (= low quality bases).

Hands-on: Quality control

1. Run Trim Galore! tool with
   • “Is this library paired- or single-end?” to Single-end
   • “Reads in FASTQ format” to the imported file
   • “Trim Galore! advanced settings” to Full parameter list
   • “Trim low-quality ends from reads” to 15
   • “Overlap with adapter sequence required to trim a sequence” to 3

   Tip: Importing data from a data library

   If your FASTQ files cannot be selected, you might check whether their format is FASTQ with Sanger-scaled quality values (fastqsanger). You can edit the data type by clicking on the pencil symbol.

Step 2: Mapping of the reads

In order to figure where the sequenced DNA fragments originated from in the genome, the short reads must be aligned to the reference genome. This is equivalent to solving a jigsaw puzzles, but unfortunately, not all pieces are unique. In principle, you could do a BLAST analysis to figure out where the sequenced pieces fit best in the known genome. Aligning millions of short sequences this way may, however, take a couple of weeks.

Running Bowtie2

Nowadays, there are many read alignment programs for shotgun sequenced DNA, Bowtie2 being one of them.

Hands-on: Mapping

1. Bowtie2 tool with
   • “Is this single or paired library” to Single-end
   • “FASTA/Q file” to the Trim Galore! output with the trimmed reads
   • “Will you select a reference genome from your history or use a built-in index?” to Use a built-in genome index
   • “Select reference genome” to Human (Homo sapiens): hg18

   Question

   1. How many reads where mapped?

   Solution

   1. This information can be accessed by clicking on the resulting history entry. You can see some basic mapping statistics once the alignment is completed. 16676 (66.96%) were mapped exactly 1 time and 7919 (31.80%) aligned >1 times. The overall alignment rate is then 98.76%.

The read alignment step with bowtie2 resulted in a compressed, binary file (BAM) that is not human-readable. It’s like the zipped version of a text file.

We will show you two ways to inspect the file:

1. Visualization using a Genome Browser
2. Converting the binary format into its text file equivalent

Visualization using a Genome Browser

Hands-on: Visualization of the reads in IGV

1. Click on the display with IGV local to load the reads into the IGV browser
2. Zoom at the start of chromosome 11 (or chr11:1,562,200-1,591,483)

The reads have a direction: they are mapped to the forward or reverse strand, respectively. When hovering over a read, extra information is displayed

Question

1. Some reads have colored lines included. What is this?

Solution

1. Try to zoom in in one of those lines and you will see the answer!

Comment

Because the number of reads over a region can be quite large, the IGV browser by default only allows to see the reads that fall into a small window. This behaviour can be changed in the IGV preferences panel.

Inspection of the SAM format

As mentioned above, you can convert the binary BAM file into a simple (but large!) text file, which is called a SAM (Sequence Alignment Map) file.

Hands-on: Conversion into a SAM file

1. BAM-to-SAM tool with
   • “BAM File to Convert” to the file generated by Bowtie2
   • “Header options” to Include header in SAM output
2. Inspect the file by clicking on eye icon

A SAM file is a file with

• A header with the chromosome names and lengths
• A file content as a tabular file with the location and other information of each read found in the FASTQ file and the mapping information

Question

1. Which information do you find in a SAM/BAM file? What is the additional information compared to a FASTQ file.

Solution

1. Sequences and Quality information, like FASTQ
2. Mapping information; Location of the read on the chromosome; Mapping quality …
3. For more information please see https://en.wikipedia.org/wiki/SAM_(file_format)

Step 3: ChIP-seq Quality Control

We already checked the quality of the raw sequencing reads in the first step. Now we would like to test the quality of the ChIP-seq preparation, to know if your ChIP-seq samples are more enriched than the control (input) samples.

Correlation between samples

To assess the similarity between the replicates of the ChIP and the input, respectively, it is a common technique to calculate the correlation of read counts on different regions for all different samples. We expect that the replicates of the ChIP-seq experiments should be clustered more closely to each other than the replicates of the input sample. That is, because the input samples should not have enriched regions included - remember the immuno-precipitation step was skiped during the sample preparation.

To compute the correlation between the samples we are going to to use the QC modules of deepTools (http://deeptools.readthedocs.io/), a software package for the QC, processing and analysis of NGS data. Before computing the correlation a time consuming step is required, which is to compute the read coverage over a large number of regions from each BAM file. For this we will use the tool multiBamSummary tool.

To do that, we need at first to catch up for all our samples and re-run the previous steps (quality control and mapping) on each sample. To save time, we already did that and we can now work directly on the BAM files of the 8 samples

Hands-on: Correlation between samples

1. Create a new history
2. Import the 8 BAM files from Zenodo or from the data library into the history
   • patient1_ChIP_ER_good_outcome.bam
   • patient1_input_good_outcome.bam
   • patient2_ChIP_ER_good_outcome.bam
   • patient2_input_good_outcome.bam
   • patient3_ChIP_ER_poor_outcome.bam
   • patient3_input_poor_outcome.bam
   • patient4_ChIP_ER_poor_outcome.bam
   • patient4_input_poor_outcome.bam
3. multiBamSummary tool with
   • “Sample order matters” to No
   • “Bam file” to the 8 imported BAM files
   • “Choose computation mode” to Bins

   • “Bin size in bp” to 100

     This corresponds to the length of the fragments that were sequenced; it is not the read length!

   • “Distance between bins” to 500000 (to reduce the computation time for the tutorial)
   • “Region of the genome to limit the operation to” to chr1 (to reduce the computation time for the tutorial)

   Using these parameters, the tool will take bins of 100 bp separated by 500,000. For each bin the overlapping reads in each sample will be computed

4. plotCorrelation tool with
   • “Matrix file from the multiBamSummary tool” to the generated multiBamSummary output

   To compute and visualize the sample correlation we use plotCorrelation from deepTools. This is a fast process that allows the user to quickly try different color combinations and outputs. Feel free to try different parameters.

Question

Open image in new tab

1. How are your samples clustered? Does that correspond to your expectations?

Solution

1. Badly, this is due to the subsampling of our data. You should expect better results from your real data.
2. Expected is that your inputs and your ChIP samples cluster together.

Comment

More information on these two tools can be found at the deepTools documentation page.

IP strength estimation

To evaluate the quality of the immuno-precipitation step, we can compute the IP strength. It determines how well the signal in the ChIP-seq sample can be differentiated from the background distribution of reads in the control sample. To do that we take the data for one Patient and compare the input sample and the ChIP-seq sample.

Comment

For more information on how the IP strength is estimated, you can check the deepTools documentation page.

Hands-on: IP strength estimation

1. plotFingerprint tool with
   • “Sample order matters” to No
   • “Bam file” to patient1_input_good_outcome and patient1_ChIP_ER_good_outcome
   • “Region of the genome to limit the operation to” to chr1

The plotFingerprint tool generates a fingerprint plot. You need to intepret it to know the IP strength. The deepTools documentation explains it clearly:

Open image in new tab

Question

Open image in new tab

1. What do you think about the quality of the IP for this experiment?

Solution

The difference between input and ChIP signal is not totally clear. 20% of chromosome 1 are not sequenced at all and the ChIP signal is only slightly more enrichted then the input.

Hands-on: (Optional) IP strength estimation (other samples)

1. Run the same analysis on data of the 3 other patients

Step 4: Normalization

We would like to know where the binding sites of the estrogen receptor are located. For this we need to extract which parts of the genome have been enriched (more reads mapped) within the samples that underwent immunoprecipitation.

For the normalization we have two options.

1. Normalization by sequencing depth
2. Normalization by input file

Generation of coverage files normalized by sequencing depth

We first need to make the samples comparable. Indeed, the different samples have usually a different sequencing depth, i.e. a different number of reads. These differences can bias the interpretation of the number of reads mapped to a specific genome region.

Hands-on: Coverage file normalization

1. IdxStats tool with
   • “BAM file” to “Multiple datasets”: patient1_input_good_outcome and patient1_ChIP_ER_good_outcome

   Question

   1. What is the output of this tool?
   2. How many reads has been mapped on chr2 for the input and for the ChIP-seq samples?

   Solution

   1. This tool estimates how many reads mapped to which chromosome. Furthermore, it tells the chromosome lengths and naming convention (with or without ‘chr’ in the beginning)
   2. 1,089,370 for ChIP-seq samples and 1,467,480 for the input

2. bamCoverage tool with
   • “BAM file” to “Multiple datasets”: patient1_input_good_outcome and patient1_ChIP_ER_good_outcome
   • “Bin size in bases” to 25
   • “Scaling/Normalization method” to Normalize coverage to 1x
   • “Effective genome size” to hg19 (2451960000)
   • “Coverage file format” to bedgraph

   Question

   1. What are the different columns of a bedgraph file?

   Solution

   1. chrom, chromStart, chromEnd and a data value

3. bamCoverage tool with the same parameters but to generate a bigWig output file

4. IGV tool to inspect both signal coverages (input and ChIP samples) in IGV

   Question

   1. What is a bigWig file?

   Solution

   A bigWig file is a compressed bedgraph file. Similar in relation as BAm to SAM, but this time just for coverage data. This means bigWig and bedgraph files are much smaller than BAM or SAM files.

Generation of input-normalized coverage files and their visualization

To extract only the information induced by the immunoprecipitation, we normalize for each patient the coverage file for the sample that underwent immunoprecipitation by the coverage file for the input sample. Here we use the tool bamCompare which compare 2 BAM files while caring for sequencing depth normalization.

Hands-on: Generation of input-normalized coverage files

1. bamCompare tool with
   • “First BAM file (e.g. treated sample)” to patient1_ChIP_ER_good_outcome
   • “Second BAM file (e.g. control sample)” to patient1_input_good_outcome
   • “Bin size in bases” to 50
   • “How to compare the two files” to Compute log2 of the number of reads ratio
   • “Coverage file format” to bedgraph

   • “Region of the genome to limit the operation to” to chr11 (to reduce the computation time for the tutorial)

     Question

     1. What does mean a positive or a negative value in the 4th column?

     Solution

     1. The 4th column contains the log2 of the number of reads ratio between the ChIP-seq sample and the input sample. A positive value means that the coverage on the portion is more important in the ChIP-seq sample than in the input sample

2. bamCompare tool with the same parameters but to generate a bigWig output file

3. IGV tool to inspect the log2 ratio

   Remember that the bigWig file contains only the signal on chromosome 11!

Step 5: Detecting enriched regions (peak calling)

We can also call the enriched regions, or peaks, found in the ChIP-seq samples.

Hands-on: Peak calling

1. MACS2 callpeak tool with
   • “ChIP-Seq Treatment File” to patient1_ChIP_ER_good_outcome
   • “ChIP-Seq Control File” to patient1_input_good_outcome
   • “Effective genome size” to H. sapiens (2.7e9)
   • “Outputs” to Summary page (html)

   Comment

   The advanced options may be adjusted, depending of the samples. If your ChIP-seq experiment targets regions of broad enrichment, e.g. non-punctuate histone modifications, select calling of broad regions. If your sample has a low duplication rate (e.g. below 10%), you might keep all duplicate reads (tags). Otherwise, you might use the ‘auto’ option to estimate the maximal allowed number of duplicated reads per genomic location.

2. IGV tool to inspect with the signal coverage and log2 ratio tracks

The called peak regions can be filtered by, e.g. fold change, FDR and region length for further downstream analysis.

Step 6: Plot the signal on the peaks between samples

Plotting your region of interest will involve using two tools from the deepTools suite.

• computeMatrix : Computes the signal on given regions, using the bigwig coverage files from different samples.
• plotHeatmap : Plots heatMap of the signals using the computeMatrix output.

ptionally, you can also use plotProfileto create a profile plot using to computeMatrix output.

computeMatrix

Hands-on: Visualization of the coverage

1. UCSC Main tool with
   • “assembly” to hg18
   • “track” to RefSeq genes
   • “region” to position with chr11
   • “output format” to BED
   • “Send output to” to Galaxy
2. computeMatrix tool with
   • “Regions to plot” to the imported UCSC file
   • “Score file” to the bigwig file generated by bamCompare

   • “computeMatrix has two main output options” to scale-regions

     This option stretches or shrinks all regions in the BED file (here: genes) to the same length (bp) as indicated by the user

   • “Show advanced options” to yes
   • “Convert missing values to 0?” to Yes

   This tool prepares a file with scores per genomic region, which is required as input for the next tool.

plotHeatmap

Hands-on: Visualization of the coverage

1. plotHeatmap tool with
   • “Matrix file from the computeMatrix tool” to the generated matrix
   • “Show advanced options” to yes
   • “Did you compute the matrix with more than one groups of regions?” to the correct setting

Conclusion

Open image in new tab

Additional exercise (if you have finished all above)

Additional Quality control : GC bias assessment

A common problem of PCR-based protocols is the observation that GC-rich regions tend to be amplified more readily than GC-poor regions. We need to check that our samples do not have more reads from regions of the genome with high GC.

Comment

GC bias was for many years a big problem, but recent advances in sample preparation have solved this problem to a degree that you can skip this step more often.

For practical reasons, we will focus here only on one of our BAM files. With real data you should repeat these steps for all your samples.

Question

1. Can you guess why it makes more sense to check the input files for GC bias?

Solution

1. We only want to assess the bias induced by the PCR-based protocols. This is not possible with the ChIP samples, as the enriched regions (binding sites) can have a potential GC enrichment on their own.

Hands-on: GC bias assessment

1. computeGCbias tool with
   • “BAM file” to patient1_input_good_outcome
   • “Reference genome” to locally cached
   • “Using reference genome” to Human (Homo sapiens): hg18
   • “Effective genome size” to hg19 (2451960000)
   • “Fragment length used for the sequencing” to 300
   • “Region of the genome to limit the operation to” to chr1 (to reduce the computation time for the tutorial)

   Question

   Open image in new tab
   
   

   1. Does this dataset have a GC bias?

   Solution

   1. There is no significantly more reads in the GC-rich regions.

Plotting heatmap from multiple samples with clustering

Hands-on: plotting multiple samples

1. Run bamCompare tool with same parameters as above, for all 4 patients:
   • “First BAM file (e.g. treated sample)” to patient2_ChIP_ER_good_outcome, patient3_ChIP_ER_good_outcome, patient4_ChIP_ER_good_outcome
   • “Second BAM file (e.g. control sample)” to patient2_input_good_outcome, patient3_input_good_outcome, patient4_input_good_outcome

2. Perform peak calling again using treatment file : patient2_ChIP_ER_good_outcome and control patient2_input_good_outcome, using macs2 parameters same as above.

3. Concatenate the outputs (summits in BED) from patient1 and patient2 using Operate on Genomic Intervals –> Concatenate

4. Sort the output Operate on Genomic Intervals –> sortBED

5. Merge the overlapping intervals using Operate on Genomic Intervals –> MergeBED

6. computeMatrix tool with the same parameters but:
   • Regions to plot : select the merged bed from above
   • Output option : reference-point
   • The reference point for the plotting: center of region
   • Distance upstream of the start site of the regions defined in the region file : 3000
   • Distance downstream of the end site of the given regions: 3000

   With this option, it considers only those genomic positions before (downstream) and/or after (upstream) a reference point (e.g. TSS, which corresponds to the annotated gene start in our case)

7. plotHeatmap tool with
   • “Matrix file from the computeMatrix tool” to the generated matrix
   • “Show advanced options” to yes
   • “Did you compute the matrix with more than one groups of regions?” to No, I used only one group
   • “Clustering algorithm” to Kmeans clustering Inspect the output

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• ChIP-seq data requires multiple methods of quality assessment to ensure that the data is of high quality.

• Multiple normalization methods exists depending on the availability of input data.

• Heatmaps containing all genes of an organism can be easily plotted given a BED file and a coverage file.

Frequently Asked Questions

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Citing this Tutorial

1. Friederike Dündar, Anika Erxleben, Bérénice Batut, Vivek Bhardwaj, Fidel Ramirez, Identification of the binding sites of the Estrogen receptor (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{epigenetics-estrogen-receptor-binding-site-identification,
author = "Friederike Dündar and Anika Erxleben and Bérénice Batut and Vivek Bhardwaj and Fidel Ramirez",
	title = "Identification of the binding sites of the Estrogen receptor (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools:
- name: deeptools_bam_compare
  owner: bgruening
  revisions: a1ca9bccc7f2
  tool_panel_section_label: deepTools
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: deeptools_bam_coverage
  owner: bgruening
  revisions: 5d11599b8a7d
  tool_panel_section_label: deepTools
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: deeptools_compute_gc_bias
  owner: bgruening
  revisions: 29fcfd36e90a
  tool_panel_section_label: deepTools
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: deeptools_compute_matrix
  owner: bgruening
  revisions: fd1275e01605
  tool_panel_section_label: deepTools
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: deeptools_multi_bam_summary
  owner: bgruening
  revisions: 2d466b530754
  tool_panel_section_label: deepTools
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: deeptools_plot_correlation
  owner: bgruening
  revisions: f264afa9fa6f
  tool_panel_section_label: deepTools
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: deeptools_plot_fingerprint
  owner: bgruening
  revisions: f8fc4e5aff9d
  tool_panel_section_label: deepTools
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: deeptools_plot_heatmap
  owner: bgruening
  revisions: 512155688d98
  tool_panel_section_label: deepTools
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: trim_galore
  owner: bgruening
  revisions: 1bf4789584dc
  tool_panel_section_label: FASTA/FASTQ
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: bam_to_sam
  owner: devteam
  revisions: 88eedb4abea0
  tool_panel_section_label: SAM/BAM
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: bowtie2
  owner: devteam
  revisions: 66f992977578
  tool_panel_section_label: Mapping
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: fastqc
  owner: devteam
  revisions: f2e8552cf1d0
  tool_panel_section_label: FASTA/FASTQ
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: samtools_idxstats
  owner: devteam
  revisions: 88b8c2916784
  tool_panel_section_label: SAM/BAM
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: macs2
  owner: iuc
  revisions: f5d67c722d67
  tool_panel_section_label: Peak Calling
  tool_shed_url: https://toolshed.g2.bx.psu.edu/

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