Time-stamp: <2018-03-02 10:45:34 Cheng-Kai Shiau>
In higher eukaryotes, the generation of RNA isoforms, including alternative splicing events (AS) and alternative transcript products (AT), from one single gene increases functional and regulatory diversities. Identification of these RNA isoforms is essential for genomic studies. However, no tool can provide comprehensive alternative event annotation including both AS and AT. Here we develop a tool named Comprehensive Alternative Transcripts Atlas based oN Annotation (CATANA) to identify all 10 known AS and AT events.
Not required! CATANA is written by Perl without additional packages. Installation is not required!
perl CATANA.pl [-i] <Input GTF/GFF3 file name> [-o] <Folder name for output, optional>
[-l] <Log file name, optional> [-d] <Debug message, optional>
-i/--infile FILENAME
This is the only one required parameter for CATANA. The gene annotation stored in GTF/GFF3 format will be parsed. CATANA will automatically recognize which format it is to prevent manual error.
-o/--outdir DIRNAME
This is optional parameter. The default output directory for holding all 10 alternative events output is named 'alternative_event_annotation'. CATANA will stop if the folder exists to prevent any accidental mistake.
-l/--log
This is optional parameter. By default, the log will not be output. The log file is created when the log file name is given.
-d/--debug
This is optional parameter. By default, the debug message is turned off. Set this parameter to 1 to dump out debug message.
perl CATANA.pl -i manually_created_alternative_events/simulated_SE.gff3 -l test.txt
This command execute CATANA to process simulated skipped exon example GFF3 contained under folder named 'manually_created_alternative_events' with default rather than given output folder name, and then dump processing log into file named 'test.txt'.
There are two tools under CATANA folder. One is named 'counting_gene_IDs.sh', and the other one is GFF3 simulator.
'counting_gene_IDs.sh' is a BASH shell script using 'awk' to calculate the number of unique gene names under the given output folder.
GFF3 simulator is separated into 10 short R scripts. Each R script is used to simulate a specific AS or AT event. We have already generated a set of all 10 AS and AT events with their graphic gene models shown by IGV. All the R scripts, simulated GFF files and figures are stored under folder named 'manually_created_alternative_events'.