Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38

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Workflow Type: Galaxy

CLIP-Seq data analysis from pre-processing to motif detection

Associated Tutorial

This workflows is part of the tutorial Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 , available in the GTN

Thanks to...

Tutorial Author(s): Florian Heyl, Daniel Maticzka, Bérénice Batut

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SEEK ID: https://dev.workflowhub.eu/workflows/1285?version=2

Inputs

ID Name Description Type
Annotation Reference File for RCAS #main/Annotation Reference File for RCAS n/a
  • File
Background #main/Background n/a
  • array containing
    • File
Enriched set as a paired-end reads collection #main/Enriched set as a paired-end reads collection n/a
  • array containing
    • File
Genome Chromosome Sizes #main/Genome Chromosome Sizes n/a
  • File

Steps

ID Name Description
4 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
5 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1
6 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
7 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1
8 UMI-tools extract toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2
9 UMI-tools extract toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2
10 RNA STAR toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1
11 RNA STAR toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1
12 UMI-tools deduplicate toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy2
13 UMI-tools deduplicate toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy2
14 Extract alignment ends toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2
15 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
16 PEAKachu toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.2
17 Merge collections __MERGE_COLLECTION__
18 Extract alignment ends toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2
19 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
20 Sort sort1
21 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
22 Sort collection __SORTLIST__
23 Sort sort1
24 Create a BedGraph of genome coverage toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0
25 bedtools SlopBed toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1
26 plotFingerprint toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.1.0.0
27 multiBamSummary toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.1.0.0
28 Create a BedGraph of genome coverage toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0
29 Wig/BedGraph-to-bigWig wig_to_bigWig
30 Extract Genomic DNA toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy2
31 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
32 plotCorrelation toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0
33 Wig/BedGraph-to-bigWig wig_to_bigWig
34 MEME-ChIP toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1
35 RCAS toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4

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_2 #main/_anonymous_output_2 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

Version History

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

Added/updated 4 files


Open master f7bed96

9.0 (earliest) Created 25th Jun 2024 at 11:19 by Helena Rasche

Added/updated 4 files


Frozen 9.0 df44e92
help Creators and Submitter
Creators
Not specified
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Discussion Channel
GTN Matrix
Tools
FastQC
Cutadapt
UMI-tools
STAR
Peakachu
BEDTools
DeepTools
MEME
RCAS
License
Creative Commons Attribution 4.0 International
Activity

Views: 599   Downloads: 182

Created: 25th Jun 2024 at 11:19

Last updated: 25th Jun 2024 at 11:19

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