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

Includes Galaxy Workflow Tests

Thanks to...

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

SEEK ID: https://dev.workflowhub.eu/workflows/1175?version=2

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