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
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flowchart TD 0["ℹ️ Input Dataset\nG1E_input_R1_downsampled_SRR507859.fastqsanger"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nG1E_input_R2_downsampled_SRR507860.fastqsanger"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nG1E_Tal1_R1_downsampled_SRR492444.fastqsanger"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nG1E_Tal1_R2_downsampled_SRR492445.fastqsanger"]; style 3 stroke:#2c3143,stroke-width:4px; 4["ℹ️ Input Dataset\nMegakaryocyte_input_R1_downsampled_SRR492453.fastqsanger"]; style 4 stroke:#2c3143,stroke-width:4px; 5["ℹ️ Input Dataset\nMegakaryocyte_input_R2_downsampled_SRR492454.fastqsanger"]; style 5 stroke:#2c3143,stroke-width:4px; 6["ℹ️ Input Dataset\nMegakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger"]; style 6 stroke:#2c3143,stroke-width:4px; 7["ℹ️ Input Dataset\nMegakaryocytes_Tal1_R2_downsampled_SRR549007.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["FastQC"]; 0 -->|output| 9; 10["Trimmomatic"]; 0 -->|output| 10; 11["FastQC"]; 1 -->|output| 11; 12["Trimmomatic"]; 1 -->|output| 12; 13["FastQC"]; 2 -->|output| 13; 14["Trimmomatic"]; 2 -->|output| 14; 15["FastQC"]; 3 -->|output| 15; 16["Trimmomatic"]; 3 -->|output| 16; 17["FastQC"]; 4 -->|output| 17; 18["Trimmomatic"]; 4 -->|output| 18; 19["FastQC"]; 5 -->|output| 19; 20["Trimmomatic"]; 5 -->|output| 20; 21["FastQC"]; 6 -->|output| 21; 22["Trimmomatic"]; 6 -->|output| 22; 23["FastQC"]; 7 -->|output| 23; 24["Trimmomatic"]; 7 -->|output| 24; 25["FastQC"]; 10 -->|fastq_out| 25; 26["Map with BWA"]; 10 -->|fastq_out| 26; 27["FastQC"]; 12 -->|fastq_out| 27; 28["Map with BWA"]; 12 -->|fastq_out| 28; 29["FastQC"]; 14 -->|fastq_out| 29; 30["Map with BWA"]; 14 -->|fastq_out| 30; 31["FastQC"]; 16 -->|fastq_out| 31; 32["Map with BWA"]; 16 -->|fastq_out| 32; 33["FastQC"]; 18 -->|fastq_out| 33; 34["Map with BWA"]; 18 -->|fastq_out| 34; 35["FastQC"]; 20 -->|fastq_out| 35; 36["Map with BWA"]; 20 -->|fastq_out| 36; 37["FastQC"]; 22 -->|fastq_out| 37; 38["Map with BWA"]; 22 -->|fastq_out| 38; 39["FastQC"]; 24 -->|fastq_out| 39; 40["Map with BWA"]; 24 -->|fastq_out| 40; 41["Samtools idxstats"]; 26 -->|bam_output| 41; 42["Samtools idxstats"]; 28 -->|bam_output| 42; 43["Samtools idxstats"]; 30 -->|bam_output| 43; 44["bamCompare"]; 30 -->|bam_output| 44; 26 -->|bam_output| 44; 45["Samtools idxstats"]; 32 -->|bam_output| 45; 46["plotFingerprint"]; 26 -->|bam_output| 46; 28 -->|bam_output| 46; 30 -->|bam_output| 46; 32 -->|bam_output| 46; 47["MACS2 callpeak"]; 26 -->|bam_output| 47; 28 -->|bam_output| 47; 30 -->|bam_output| 47; 32 -->|bam_output| 47; 48["bamCompare"]; 32 -->|bam_output| 48; 28 -->|bam_output| 48; 49["Samtools idxstats"]; 34 -->|bam_output| 49; 50["Samtools idxstats"]; 36 -->|bam_output| 50; 51["Samtools idxstats"]; 38 -->|bam_output| 51; 52["bamCompare"]; 38 -->|bam_output| 52; 34 -->|bam_output| 52; 53["Samtools idxstats"]; 40 -->|bam_output| 53; 54["multiBamSummary"]; 26 -->|bam_output| 54; 28 -->|bam_output| 54; 30 -->|bam_output| 54; 32 -->|bam_output| 54; 34 -->|bam_output| 54; 36 -->|bam_output| 54; 38 -->|bam_output| 54; 40 -->|bam_output| 54; 55["plotFingerprint"]; 34 -->|bam_output| 55; 36 -->|bam_output| 55; 38 -->|bam_output| 55; 40 -->|bam_output| 55; 56["MACS2 callpeak"]; 34 -->|bam_output| 56; 36 -->|bam_output| 56; 38 -->|bam_output| 56; 40 -->|bam_output| 56; 57["bamCompare"]; 40 -->|bam_output| 57; 36 -->|bam_output| 57; 58["computeMatrix"]; 44 -->|outFileName| 58; 48 -->|outFileName| 58; 47 -->|output_narrowpeaks| 58; 59["plotCorrelation"]; 54 -->|outFile| 59; 60["bedtools Intersect intervals"]; 47 -->|output_narrowpeaks| 60; 56 -->|output_narrowpeaks| 60; 0d48a613-5d3c-46bb-8795-9bb35399ae82["Output\noutput_overlapping_peaks"]; 60 --> 0d48a613-5d3c-46bb-8795-9bb35399ae82; style 0d48a613-5d3c-46bb-8795-9bb35399ae82 stroke:#2c3143,stroke-width:4px; 61["bedtools Intersect intervals"]; 47 -->|output_narrowpeaks| 61; 56 -->|output_narrowpeaks| 61; d7a28606-a897-45f5-b784-abbf499a62e9["Output\noutput_g1e_peaks"]; 61 --> d7a28606-a897-45f5-b784-abbf499a62e9; style d7a28606-a897-45f5-b784-abbf499a62e9 stroke:#2c3143,stroke-width:4px; 62["bedtools Intersect intervals"]; 56 -->|output_narrowpeaks| 62; 47 -->|output_narrowpeaks| 62; a924e63e-5f80-4ff0-9a31-99e481d5a825["Output\noutput_megakaryocyte_peaks"]; 62 --> a924e63e-5f80-4ff0-9a31-99e481d5a825; style a924e63e-5f80-4ff0-9a31-99e481d5a825 stroke:#2c3143,stroke-width:4px; 63["computeMatrix"]; 52 -->|outFileName| 63; 57 -->|outFileName| 63; 56 -->|output_narrowpeaks| 63; 64["plotHeatmap"]; 58 -->|outFileName| 64; 65["plotHeatmap"]; 63 -->|outFileName| 65;
Inputs
Input | Label |
---|---|
G1E_input_R1_downsampled_SRR507859.fastqsanger | G1E_input_R1_downsampled_SRR507859.fastqsanger |
G1E_input_R2_downsampled_SRR507860.fastqsanger | G1E_input_R2_downsampled_SRR507860.fastqsanger |
G1E_Tal1_R1_downsampled_SRR492444.fastqsanger | G1E_Tal1_R1_downsampled_SRR492444.fastqsanger |
G1E_Tal1_R2_downsampled_SRR492445.fastqsanger | G1E_Tal1_R2_downsampled_SRR492445.fastqsanger |
Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger | Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger |
Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger | Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger |
Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger | Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger |
Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger | Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger |
RefSeq_gene_annotations_mm10.bed | RefSeq_gene_annotations_mm10.bed |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0 | bedtools Intersect intervals | |
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0 | bedtools Intersect intervals | |
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0 | bedtools Intersect intervals |
Tools
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
- Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
- Click on galaxy-upload Import at the top-right of the screen
- 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”
- 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 |
---|---|---|---|
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