As with all bioinformatic methods there are always multiple programs for completing the same task. Here we will look at another fusion detection program called EricScript (see: Benelli M, Pescucci C, Marseglia G, Severgnini M, Torricelli F, Magi A. Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript. Bioinformatics. 2012; 28(24): 3232-3239)
We will run this on the same data as tophat-fusion. The DB’s and software you need for this program have already been installed in MolBioCloud.
cd ~/Desktop/fusion ericscript.pl -db ericscript_db_homosapiens_ensembl84 -name MCF7 -o ES_MCF7 SRR064286_1.fastq SRR064286_2.fastq
This takes about 35 minutes to process the data. (Much faster than tophat)
For a review on fusion genes tools see (http://www.nature.com/articles/srep21597)