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

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• Import to another server (≥23.0+ only!)

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;
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  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;
  cf5bede4-89ea-4859-9dc7-36d32c06e5d6["Output\noutput_overlapping_peaks"];
  60 --> cf5bede4-89ea-4859-9dc7-36d32c06e5d6;
  style cf5bede4-89ea-4859-9dc7-36d32c06e5d6 stroke:#2c3143,stroke-width:4px;
  61["bedtools Intersect intervals"];
  47 -->|output_narrowpeaks| 61;
  56 -->|output_narrowpeaks| 61;
  3c376109-e191-4ab9-a90a-6284f4b3078c["Output\noutput_g1e_peaks"];
  61 --> 3c376109-e191-4ab9-a90a-6284f4b3078c;
  style 3c376109-e191-4ab9-a90a-6284f4b3078c stroke:#2c3143,stroke-width:4px;
  62["bedtools Intersect intervals"];
  56 -->|output_narrowpeaks| 62;
  47 -->|output_narrowpeaks| 62;
  8fe26d7b-6969-4f71-8502-b53052744c4d["Output\noutput_megakaryocyte_peaks"];
  62 --> 8fe26d7b-6969-4f71-8502-b53052744c4d;
  style 8fe26d7b-6969-4f71-8502-b53052744c4d 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

Outputs

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

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:

Version History

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