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.
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 | fastqsanger |
| report | report | n/a | txt |
| html_file | html_file | n/a | html |
| text_file | text_file | n/a | txt |
| out | out | n/a | fasta |
| html_file | html_file | n/a | html |
| text_file | text_file | n/a | txt |
| mapped_bed | mapped_bed | n/a | bed |
| unmapped_fasta | unmapped_fasta | n/a | fasta |
| segments_bed | segments_bed | n/a | bed |
| merged_bed | merged_bed | n/a | tabular |
| loci | loci | n/a | tabular |
| chimeras | chimeras | n/a | tabular |
| interactions | interactions | n/a | tabular |
| sqlitedb | sqlitedb | n/a | sqlite |
Creators and SubmitterLicense
Activity
Views: 125 Downloads: 8
Created: 3rd Nov 2020 at 19:46
Last used: 20th Jan 2021 at 15:54
Tags AttributionsNone
Related items
Teams: usegalaxy-eu
Organizations: Albert-Ludwigs-Universität Freiburg
https://orcid.org/0000-0002-5192-126X
No description specified
Space: Independent Teams
Public web page: https://usegalaxy.eu
