ATAC-seq GTM

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Workflow Type: Galaxy

atac-seq

Associated Tutorial

This workflows is part of the tutorial ATAC-seq GTM, available in the GTN

Thanks to...

Tutorial Author(s): Lucille Delisle, Maria Doyle, Florian Heyl

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1169?version=2

Inputs

ID Name Description Type
ATAC R1 read in fastq(.gz) format #main/ATAC R1 read in fastq(.gz) format n/a
  • File
ATAC R2 read in fastq(.gz) format #main/ATAC R2 read in fastq(.gz) format n/a
  • File
bed file with genes #main/bed file with genes n/a
  • File
ctcf peaks #main/ctcf peaks n/a
  • File

Steps

ID Name Description
4 Filter Filter1
5 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
6 ATAC remove nextera adapters with cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5
7 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
8 bedtools Intersect intervals toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0
9 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
10 Bowtie2 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0
11 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
12 Filter BAM ATAC toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
13 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
14 bedtools BAM to BED toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0
15 Paired-end histogram toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1
16 MACS2 callpeak toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6
17 Wig/BedGraph-to-bigWig wig_to_bigWig
18 computeMatrix toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0
19 pyGenomeTracks toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6
20 computeMatrix toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0
21 plotHeatmap toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1
22 plotHeatmap toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_12 #main/_anonymous_output_12 n/a
  • File
_anonymous_output_13 #main/_anonymous_output_13 n/a
  • File
_anonymous_output_14 #main/_anonymous_output_14 n/a
  • File
_anonymous_output_15 #main/_anonymous_output_15 n/a
  • File
_anonymous_output_16 #main/_anonymous_output_16 n/a
  • File
_anonymous_output_17 #main/_anonymous_output_17 n/a
  • File
_anonymous_output_18 #main/_anonymous_output_18 n/a
  • File
_anonymous_output_19 #main/_anonymous_output_19 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_20 #main/_anonymous_output_20 n/a
  • File
_anonymous_output_21 #main/_anonymous_output_21 n/a
  • File
_anonymous_output_22 #main/_anonymous_output_22 n/a
  • File
_anonymous_output_23 #main/_anonymous_output_23 n/a
  • File
_anonymous_output_24 #main/_anonymous_output_24 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File
computeMatrix on input dataset(s): Matrix #main/computeMatrix on input dataset(s): Matrix n/a
  • File
plotHeatmap on input dataset(s): Image #main/plotHeatmap on input dataset(s): Image n/a
  • File

Version History

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

Added/updated 4 files


Open master 757bc20

20.0 (earliest) Created 25th Jun 2024 at 11:05 by Helena Rasche

Added/updated 4 files


Frozen 20.0 6e462f4
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Discussion Channel
GTN Matrix
Tools
FastQC
Cutadapt
BEDTools
Bowtie 2
BamTools
SeqCode
MACS
DeepTools
pyGenomeTracks
License
Creative Commons Attribution 4.0 International
Activity

Views: 429   Downloads: 148

Created: 25th Jun 2024 at 11:05

Last updated: 25th Jun 2024 at 11:05

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