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Fusion Detection Using EricScript

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)