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

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Workflow Type: Galaxy

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

Associated Tutorial

This workflows is part of the tutorial Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1), available in the GTN

Features

Thanks to...

Tutorial Author(s): Mallory Freeberg, Mo Heydarian, Vivek Bhardwaj, Joachim Wolff, Anika Erxleben

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1175?version=1

Inputs

ID Name Description Type
G1E_Tal1_R1_downsampled_SRR492444.fastqsanger G1E_Tal1_R1_downsampled_SRR492444.fastqsanger n/a
  • File
G1E_Tal1_R2_downsampled_SRR492445.fastqsanger G1E_Tal1_R2_downsampled_SRR492445.fastqsanger n/a
  • File
G1E_input_R1_downsampled_SRR507859.fastqsanger G1E_input_R1_downsampled_SRR507859.fastqsanger n/a
  • File
G1E_input_R2_downsampled_SRR507860.fastqsanger G1E_input_R2_downsampled_SRR507860.fastqsanger n/a
  • File
Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger n/a
  • File
Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger n/a
  • File
Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger n/a
  • File
Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger n/a
  • File
RefSeq_gene_annotations_mm10.bed RefSeq_gene_annotations_mm10.bed n/a
  • File

Steps

ID Name Description
9 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
10 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
11 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
12 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
13 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
14 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
15 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
16 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
17 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
18 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
19 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
20 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
21 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
22 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
23 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
24 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
25 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
26 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
27 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
28 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
29 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
30 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
31 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
32 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
33 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
34 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
35 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
36 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
37 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
38 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
39 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
40 Map with BWA toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
41 Samtools idxstats toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3
42 Samtools idxstats toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3
43 Samtools idxstats toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3
44 bamCompare toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0
45 Samtools idxstats toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3
46 plotFingerprint toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0
47 MACS2 callpeak toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6
48 bamCompare toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0
49 Samtools idxstats toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3
50 Samtools idxstats toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3
51 Samtools idxstats toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3
52 bamCompare toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0
53 Samtools idxstats toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3
54 multiBamSummary toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0
55 plotFingerprint toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0
56 MACS2 callpeak toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6
57 bamCompare toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0
58 computeMatrix toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0
59 plotCorrelation toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0
60 bedtools Intersect intervals toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0
61 bedtools Intersect intervals toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0
62 bedtools Intersect intervals toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0
63 computeMatrix toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0
64 plotHeatmap toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1
65 plotHeatmap toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1

Outputs

ID Name Description Type
output_overlapping_peaks output_overlapping_peaks n/a
  • File
output_g1e_peaks output_g1e_peaks n/a
  • File
output_megakaryocyte_peaks output_megakaryocyte_peaks n/a
  • File

Version History

1.0 (latest) Created 16th Jul 2024 at 14:06 by Helena Rasche

Added/updated 4 files


Open master f525bb2

5.0 (earliest) Created 25th Jun 2024 at 11:06 by Helena Rasche

Added/updated 4 files


Frozen 5.0 47f27f4
help Creators and Submitter
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Tools
FastQC
Trimmomatic
BWA
SAMtools
DeepTools
MACS
BEDTools
License
Creative Commons Attribution 4.0 International
Activity

Views: 607   Downloads: 189

Created: 25th Jun 2024 at 11:06

Last updated: 25th Jun 2024 at 11:06

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