EricScript Readme v2.1 (Feb 2016)
Fork created by mmterpstra@github.com due to inactivity on the original forum. The version the files from is v0.5.5. This goals: run a minimal install/test on travis if possible. Feel free to submit a pull request if you think you can fix it faster and better.
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 the following software
- R: http://cran.r-project.org/
- "ada" R package: http://cran.r-project.org/web/packages/ada/index.html
- BWA: http://bio-bwa.sourceforge.net
- SAMtools (>0.1.17): http://samtools.sourceforge.net/
- bedtools (>2.15): http://code.google.com/p/bedtools/
- BLAT binaries: http://genome-test.cse.ucsc.edu/~kent/exe/
- 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 -db /PATH/TO/YOUR/DBFOLDER
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 <=82) 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 -db /PATH/TO/YOUR/DBFOLDER
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.