Workflows
These workflows are associated with Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
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.
Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)
Last updated Oct 7, 2020
Launch in Tutorial Mode
License:
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CC-BY-4.0
Tests: ✅
Results: Not yet automated
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; 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;
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: