RNA-RNA interactome data analysis - chira v1.4.3

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Workflow Type: Galaxy

RNA-RNA interactome analysis using ChiRA tool suite

Associated Tutorial

This workflows is part of the tutorial RNA-RNA interactome data analysis - chira v1.4.3, available in the GTN

Features

Thanks to...

Tutorial Author(s): Pavankumar Videm

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1291?version=2

Inputs

ID Name Description Type
annotation_gtf #main/annotation_gtf n/a
  • File
genome_fasta #main/genome_fasta n/a
  • File
reads_fastq #main/reads_fastq n/a
  • File
reference1_fasta #main/reference1_fasta n/a
  • File
reference2_fasta #main/reference2_fasta n/a
  • File

Steps

ID Name Description
5 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
6 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 ChiRA collapse toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0
9 ChiRA map toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0
10 ChiRA merge toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0
11 ChiRA qauntify toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0
12 ChiRA extract toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0
13 Query Tabular toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0

Outputs

ID Name Description Type
_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_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
chimeric_reads #main/chimeric_reads n/a
  • File
db #main/db n/a
  • File
interactions #main/interactions n/a
  • File

Version History

1.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche

Added/updated 4 files


Open master 860a9a3

2.0 (earliest) Created 25th Jun 2024 at 11:20 by Helena Rasche

Added/updated 4 files


Frozen 2.0 68591c8
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
FastQC
Cutadapt
ChiRA
License
Creative Commons Attribution 4.0 International
Activity

Views: 441   Downloads: 151

Created: 25th Jun 2024 at 11:20

Last updated: 25th Jun 2024 at 11:20

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Total size: 129 KB
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