Stable
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 |

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Views: 125 Downloads: 8
Created: 3rd Nov 2020 at 19:46
Last used: 20th Jan 2021 at 15:54


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