RNA-RNA interactome analysis using BWA-MEM

Annotation: RNA-RNA interactome analysis using ChiRA tools suite. Aligner used is BWA-MEM.

StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: Input dataset
select at runtime
Step 5: Input dataset
select at runtime
Step 6: Cutadapt
Single-end
Output dataset 'output' from step 1
Read 1 Options:
3' (End) Adapters
3' (End) Adapters 1
Enter custom sequence
Not available.
Not available.
5' (Front) Adapters
5' (Front) Adapters 1
Enter custom sequence
Not available.
Not available.
5' or 3' (Anywhere) Adapters
0
Adapter Options:
0.1
False
1
3
In the adapters but not in the reads
False
False
Filter Options:
False
False
16
0
Not available.
any
Read Modification Options:
20
0
False
Empty.
Empty.
Empty.
0
Empty.
Output Options:
True
False
False
False
False
False
False
False
Step 7: FastQC
Output dataset 'output' from step 1
select at runtime
select at runtime
select at runtime
False
Not available.
7
Step 8: ChiRA collapse
Output dataset 'out1' from step 6
Not available.
Step 9: FastQC
Output dataset 'out1' from step 6
select at runtime
select at runtime
select at runtime
False
Not available.
7
Step 10: ChiRA map
Output dataset 'out' from step 8
Split reference
Output dataset 'output' from step 2
Output dataset 'output' from step 3
BWA-MEM
Transcript strand only
12
16
18
16
1
4
1
6
6
1
100
100
50
100
Step 11: ChiRA merge
Output dataset 'mapped_bed' from step 10
Yes
Output dataset 'output' from step 4
0.7
0.9
0.7
Overlap based
1
Split reference
Output dataset 'output' from step 2
Output dataset 'output' from step 3
False
Step 12: ChiRA qauntify
Output dataset 'segments_bed' from step 11
Output dataset 'merged_bed' from step 11
0.7
10
1e-05
True
Step 13: ChiRA extract
Output dataset 'loci' from step 12
Yes
Output dataset 'output' from step 4
History
Output dataset 'output' from step 5
0.0
0.0
2
Split reference
Output dataset 'output' from step 2
Output dataset 'output' from step 3
True
Heuristic
True
5
0.0
False
150
37.0
True
Step 14: Query Tabular
workdb.sqlite
Add tables to an existing database:
select at runtime
Database Tables
Database Table 1
Output dataset 'chimeras' from step 13
Filter Dataset Input:
Filter Tabular Input Lines
Table Options:
Empty.
True
Empty.
False
Empty.
Table Indices
Modify the database:
Database Manipulation SQL Statements
True
Empty.
Yes
#
Additional Queries:
Database Manipulation SQL Statements