RNA-RNA interactome analysis using CLAN
Version 1

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

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
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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Created: 3rd Nov 2020 at 19:49

Last used: 24th Nov 2020 at 03:05

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