CICERO (Clipped-reads Extended for RNA Optimization) is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq.
Invoke the CICERO wrapper as
Cicero.sh [-n ncores] -b bamfile -g genome -r refdir [-j junctions]
Where ncores is the number of cores to be run on (with GNU parallel,
bamfile is the input bamfile, genome is GRCh37-lite, refdir is the reference file directory specific to
CICERO, and junctions is the (optional) junctions file output from RNApeg.
Once you have the output from CICERO, use the following guide to interpret the results.
- GNU parallel
- Samtools 1.3.1
- Cap3
- Blat
- Java 1.8.0
- Perl 5.10.1 with libraries:
- base
- Bio
- Carp
- Compress
- Cwd
- Data
- DBI
- diagnostics
- Digest
- English
- enum
- Exporter
- File
- FileHandle
- List
- POSIX
- strict
- Sys
- Tree
- warnings
RNApeg is required to generate a junctions file for use by CICERO. You can get RNApeg from both Docker and Singularity.
Running RNApeg via Docker:
docker run mnedmonson/public:rnapeg RNApeg.sh -b bamfile -f fasta -r refflat [-rg refflat]
Running RNApeg via Singularity:
singularity run docker://mnedmonson/public:rnapeg RNApeg.sh -b bamfile -f fasta -r refflat [-rg refflat]
Reference files are required to run CICERO. They can be found at the following location:
A demo of CICERO can be found at the following location:
Tian, L., Li, Y., Edmonson, M.N. et al. CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data. Genome Biol 21, 126 (2020). https://doi.org/10.1186/s13059-020-02043-x
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