Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

epigenetics-tal1-binding-site-identification/tal1-binding-site-identification-workflow

Author(s)
Mallory Freeberg, Mo Heydarian, Vivek Bhardwaj, Joachim Wolff, Anika Erxleben, Pavankumar Videm
version Version
2
last_modification Last updated
Sep 30, 2026
license License
CC-BY-4.0
galaxy-tags Tags
epigenetics
ChIP-seq

Features
Tutorial
hands_on Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00071
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nG1E_Tal1_R1_downsampled_SRR492444.fastqsanger"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nG1E_input_R1_downsampled_SRR507859.fastqsanger"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nG1E_Tal1_R2_downsampled_SRR492445.fastqsanger"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nG1E_input_R2_downsampled_SRR507860.fastqsanger"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nMegakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nMegakaryocyte_input_R1_downsampled_SRR492453.fastqsanger"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nMegakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nMegakaryocyte_input_R2_downsampled_SRR492454.fastqsanger"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nRefSeq_gene_annotations_mm10.bed"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["Falco"];
  0 -->|output| 9;
  10["Trimmomatic"];
  0 -->|output| 10;
  11["Falco"];
  1 -->|output| 11;
  12["Trimmomatic"];
  1 -->|output| 12;
  13["Falco"];
  2 -->|output| 13;
  14["Trimmomatic"];
  2 -->|output| 14;
  15["Falco"];
  3 -->|output| 15;
  16["Trimmomatic"];
  3 -->|output| 16;
  17["Falco"];
  4 -->|output| 17;
  18["Trimmomatic"];
  4 -->|output| 18;
  19["Falco"];
  5 -->|output| 19;
  20["Trimmomatic"];
  5 -->|output| 20;
  21["Falco"];
  6 -->|output| 21;
  22["Trimmomatic"];
  6 -->|output| 22;
  23["Falco"];
  7 -->|output| 23;
  24["Trimmomatic"];
  7 -->|output| 24;
  25["Falco"];
  10 -->|fastq_out| 25;
  26["Map with BWA"];
  10 -->|fastq_out| 26;
  27["Falco"];
  12 -->|fastq_out| 27;
  28["Map with BWA"];
  12 -->|fastq_out| 28;
  29["Falco"];
  14 -->|fastq_out| 29;
  30["Map with BWA"];
  14 -->|fastq_out| 30;
  31["Falco"];
  16 -->|fastq_out| 31;
  32["Map with BWA"];
  16 -->|fastq_out| 32;
  33["Map with BWA"];
  18 -->|fastq_out| 33;
  34["Falco"];
  18 -->|fastq_out| 34;
  35["Map with BWA"];
  20 -->|fastq_out| 35;
  36["Falco"];
  20 -->|fastq_out| 36;
  37["Map with BWA"];
  22 -->|fastq_out| 37;
  38["Falco"];
  22 -->|fastq_out| 38;
  39["Map with BWA"];
  24 -->|fastq_out| 39;
  40["Falco"];
  24 -->|fastq_out| 40;
  41["Samtools idxstats"];
  26 -->|bam_output| 41;
  42["bamCompare"];
  26 -->|bam_output| 42;
  28 -->|bam_output| 42;
  43["Samtools idxstats"];
  28 -->|bam_output| 43;
  44["Samtools idxstats"];
  30 -->|bam_output| 44;
  45["bamCompare"];
  30 -->|bam_output| 45;
  32 -->|bam_output| 45;
  46["Samtools idxstats"];
  32 -->|bam_output| 46;
  47["plotFingerprint"];
  26 -->|bam_output| 47;
  30 -->|bam_output| 47;
  32 -->|bam_output| 47;
  28 -->|bam_output| 47;
  48["MACS2 callpeak"];
  28 -->|bam_output| 48;
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  30 -->|bam_output| 48;
  26 -->|bam_output| 48;
  49["Samtools idxstats"];
  33 -->|bam_output| 49;
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  52["Samtools idxstats"];
  37 -->|bam_output| 52;
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  54["Samtools idxstats"];
  39 -->|bam_output| 54;
  55["multiBamSummary"];
  32 -->|bam_output| 55;
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  37 -->|bam_output| 55;
  39 -->|bam_output| 55;
  30 -->|bam_output| 55;
  26 -->|bam_output| 55;
  28 -->|bam_output| 55;
  56["plotFingerprint"];
  35 -->|bam_output| 56;
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  39 -->|bam_output| 56;
  33 -->|bam_output| 56;
  57["MACS2 callpeak"];
  39 -->|bam_output| 57;
  35 -->|bam_output| 57;
  37 -->|bam_output| 57;
  33 -->|bam_output| 57;
  58["plotFingerprint"];
  39 -->|bam_output| 58;
  37 -->|bam_output| 58;
  35 -->|bam_output| 58;
  33 -->|bam_output| 58;
  59["Cut"];
  48 -->|output_narrowpeaks| 59;
  60["plotCorrelation"];
  55 -->|outFile| 60;
  61["pyGenomeTracks"];
  48 -->|output_control_lambda| 61;
  48 -->|output_treat_pileup| 61;
  48 -->|output_narrowpeaks| 61;
  57 -->|output_control_lambda| 61;
  57 -->|output_treat_pileup| 61;
  57 -->|output_narrowpeaks| 61;
  8 -->|output| 61;
  bba3d5a4-7b8b-45bd-a566-8cbd8871faeb["Output\npyGenomeTracks_plot"];
  61 --> bba3d5a4-7b8b-45bd-a566-8cbd8871faeb;
  style bba3d5a4-7b8b-45bd-a566-8cbd8871faeb stroke:#2c3143,stroke-width:4px;
  62["bedtools Intersect intervals"];
  48 -->|output_narrowpeaks| 62;
  57 -->|output_narrowpeaks| 62;
  02e8b502-598e-47e5-8ee2-40afe218fe59["Output\npeaks_in_both_G1E_and_megakaryocytes"];
  62 --> 02e8b502-598e-47e5-8ee2-40afe218fe59;
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  48 -->|output_narrowpeaks| 63;
  57 -->|output_narrowpeaks| 63;
  6a996100-6efd-4d3c-ad41-a27ae607a07e["Output\npeaks_in_only_G1E"];
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  65["bedtools Intersect intervals"];
  57 -->|output_narrowpeaks| 65;
  48 -->|output_narrowpeaks| 65;
  5a4b4a8b-e784-4ebf-b16b-b2e902478d26["Output\npeaks_in_only_megakaryocytes"];
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  66["computeMatrix"];
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  64 -->|out_file1| 68;
  69["plotHeatmap"];
  66 -->|outFileName| 69;
  4a970e3a-2205-406f-a8eb-279166f5bcd4["Output\nheatmap_G1E"];
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  70["plotHeatmap"];
  67 -->|outFileName| 70;
  a9235b2b-3dbb-4f5b-a223-c2a76529bb58["Output\nheatmap_megakaryocytes"];
  70 --> a9235b2b-3dbb-4f5b-a223-c2a76529bb58;
  style a9235b2b-3dbb-4f5b-a223-c2a76529bb58 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset G1E_Tal1_R1_downsampled_SRR492444.fastqsanger
Input dataset G1E_input_R1_downsampled_SRR507859.fastqsanger
Input dataset G1E_Tal1_R2_downsampled_SRR492445.fastqsanger
Input dataset G1E_input_R2_downsampled_SRR507860.fastqsanger
Input dataset Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger
Input dataset Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger
Input dataset Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger
Input dataset Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger
Input dataset RefSeq_gene_annotations_mm10.bed

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.9+galaxy0 pyGenomeTracks
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0 bedtools Intersect intervals
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0 bedtools Intersect intervals
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0 bedtools Intersect intervals
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/4.0.0+galaxy1 plotHeatmap
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/4.0.0+galaxy1 plotHeatmap

Tools

Tool Links
Cut1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/4.0.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/4.0.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/4.0.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/4.0.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/4.0.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/4.0.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.19+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.8 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.31.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.3.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on galaxy-upload Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
7 f968236b9 2026-09-24 18:16:09 Update workflow and tests
6 6e4f348a1 2026-09-22 10:09:03 Update the TAL1 ChIP tutorial with deeptools4
5 818f00219 2020-10-06 20:46:16 Fixed JSON format.
4 473da245d 2020-10-06 20:22:32 Updated outputs in workflow and test.yml.
3 3bee4c537 2020-10-06 19:28:34 Updated inputs in workflow and test.yml.
2 e9f2fa109 2020-10-06 10:48:12 Updated workflow with tags.
1 7fe3ca36a 2020-10-05 19:06:49 Added workflow.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows