RNA-RNA interactome analysis using BWA-MEM
Version 1

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RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is BWA-MEM.

SEEK ID: https://workflowhub.eu/workflows/66?version=1

Inputs

ID Name Description Type
Reads FASTQ file Reads FASTQ file n/a n/a
1st reference FASTA file 1st reference FASTA file n/a n/a
2nd reference FASTA file 2nd reference FASTA file n/a n/a
Annotation GTF file Annotation GTF file n/a n/a
Genomic FASTA file Genomic FASTA file n/a n/a
adapters adapters runtime parameter for tool FastQC n/a
contaminants contaminants runtime parameter for tool FastQC n/a
limits limits runtime parameter for tool FastQC n/a
umi_len umi_len runtime parameter for tool ChiRA collapse n/a
adapters adapters runtime parameter for tool FastQC n/a
contaminants contaminants runtime parameter for tool FastQC n/a
limits limits runtime parameter for tool FastQC n/a
query query runtime parameter for tool ChiRA map n/a
reference reference runtime parameter for tool ChiRA map n/a
reference reference runtime parameter for tool ChiRA map n/a
add_to_database add_to_database runtime parameter for tool Query Tabular n/a

Steps

ID Name Description
0 Reads FASTQ file
1 1st reference FASTA file
2 2nd reference FASTA file
3 Annotation GTF file
4 Genomic FASTA file
5 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5
6 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
7 ChiRA collapse toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0
8 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
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
out1 out1 n/a
report report n/a
html_file html_file n/a
text_file text_file n/a
out out n/a
html_file html_file n/a
text_file text_file n/a
mapped_bed mapped_bed n/a
unmapped_fasta unmapped_fasta n/a
segments_bed segments_bed n/a
merged_bed merged_bed n/a
loci loci n/a
chimeras chimeras n/a
interactions interactions n/a
sqlitedb sqlitedb n/a

Version History

Version 1 (earliest) Created 3rd Nov 2020 at 19:46 by Pavankumar Videm

Added/updated 1 files


Open master c477acc
help Creators and Submitter
Creator
Submitter
License
GNU General Public License 3.0
Activity

Views: 829   Downloads: 32

Created: 3rd Nov 2020 at 19:46

Last used: 6th Oct 2022 at 19:54

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