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EricScript
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EricScript Readme v2.1 (Feb 2016)

Please feel free to email the author if you have any questions or issues.
matteo.benelli AT gmail.com

INFORMATION

EricScript is a software package developed in R, perl and bash scripts.
EricScript uses the BWA aligner to perform the mapping on the transcriptome reference and samtools to handle with SAM/BAM files. Recalibration of the exon junction reference is performed by using BLAT.

REQUIREMENTS

Download and install R: http://cran.r-project.org/
Download and install the "ada" R package: http://cran.r-project.org/web/packages/ada/index.html
Download and install BWA: http://bio-bwa.sourceforge.net
Download and install SAMtools (>0.1.17): http://samtools.sourceforge.net/
Download and install bedtools (>2.15): http://code.google.com/p/bedtools/
Download and install BLAT binaries: http://genome-test.cse.ucsc.edu/~kent/exe/
Download and install seqtk: https://github.com/lh3/seqtk
Be sure that all of these programs are included in your PATH.

RUNNING ERIC

Once you have downloaded EricScript, extract the package

tar -xjf ericscript.tar.bz2

Make a copy of the program folder to your favorite location. Before running for the first time EricScript, you need to make ericscript.pl executable:

chmod +x /PATH/TO/ERIC/ericscript.pl

To get information about running EricScript, digit:

/PATH/TO/ERIC/ericscript.pl --help

In order to perform chimeric transcript detection, you need to download and build the Ensembl Database of a genome. To list the available genomes, digit:

/PATH/TO/ERIC/ericscript.pl --printdb

After a reference id is selected, you need to download and build the corresponding Ensembl Database. In the example below, it's shown how to prepare the database for saccharomyces cerevisiae.

/PATH/TO/ERIC/ericscript.pl --downdb --refid saccharomyces_cerevisiae -db /PATH/TO/YOUR/DBFOLDER

You can also select a specific ensembl release (>= 70) to download

/PATH/TO/ERIC/ericscript.pl --downdb --refid saccharomyces_cerevisiae -db /PATH/TO/YOUR/DBFOLDER --ensversion 74

To run EricScript with default parameters (if parameter "refid" is not specified the analysis takes the homo sapiens species as default):

/PATH/TO/ERIC/ericscript.pl -db /PATH/TO/YOUR/DBFOLDER --refid saccharomyces_cerevisiae -name SAMPLENAME -o /PATH/TO/OUTPUT/ YOUR_FASTQ_1 YOUR_FASTQ_2

You can check if your database is up-to-date by the following:

/PATH/TO/ERIC/ericscript.pl --checkdb

OUTPUT FILES

The /PATH/TO/OUTPUT/ folder contains the results of the analysis. Predicted gene fusion products are reported in 2 files:
samplename.results.total.csv: contains all the predicted gene fusions.
samplename.results.filtered.csv: contains the predicted gene fusions with EricScore > 0.50.

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