EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data. It is able to generate synthetic gene fusions by using the EricScript simulator and calculate a number of statistical measures for evaluating gene fusion detection methods' performance with EricScript CalcStats.

In these pages, you'll find all the information you need to run EricScript.
Start your reading with Requirements, then go to Getting Started.

If you use EricScript to identify gene fusions in your RNA-seq data, please cite:

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.

To receive announcements on EricScript updates or discuss EricScript usage and results, join the eric google group.


April 28, 2016.

Download section now reports the links to download the ready-to-use EricScript databases. 


April 26, 2016.

EricScript version 0.5.5 is now available. Download it from here
It fixes (other) bugs related to the download of db data from Ensembl FTP. I suggest to the users to download the ready-to-use database (homo_sapiens) from here. Please contact me in case you are interested in other organisms.


March 2, 2016.

EricScript version 0.5.4 is now available. Download it from here
It fixes the bug related to the download of Ensembl v75 data.


March 1, 2016.

As noticed by some users, the download of ensembl v75 doesn't work well. This is due to an issue related to the xml files used to download data from Ensembl database. I will work to fix it in the next days. In the meanwhile, users interested in GRCh37 data can use Ensembl v74.


February 25, 2016.

EricScript version 0.5.3 is now bug fixed. Download it from here.
The updated version corrects a bug related to the downloading of ensembl releases <= 75.


February 19, 2016.

The ready-to-use database (homo_sapiens, Ensembl v83) is available for download here. Before using it, please use bwa index on allseq.fa file (it may take typically 1-2 hours).


February 12, 2016.

EricScript version 0.5.3 is now available. Download it from here.
This version enables the creation of EricScript database with Ensembl ≥ 70 ( ≥ GRCh37). 


October 6, 2015.

EricScript version 0.5.2 is now available. Download it from here.
This version fixes some small bugs and makes the pipeline faster.


August 26, 2014.

EricScript version 0.5.1 is now available. Download it from here.
This version allows users to download data of a specific Ensembl release, by the option --ensversion. Minimum supported Ensembl version is 76.


August 26, 2014.

EricScript version 0.5.0 is now available. Download it from here.
If you want to use this version for analysing human data, you need to update your db files (perl PATH_TO_ERIC/ericscript.pl --downdb -db PATH_TO_YOUR_ERIC_DB).
 
This version introduces the following updates:

Compatibility with the new human genome assembly (GRCh38).
• Improved sensibility in fusion detection.
• No need for genome reference data.
• EricScript Simulator is now able to generate synthetic reads for any organism available in Ensembl.


November 4, 2013.

The ready-to-use db data is up-to-date to the latest (v73) ensembl release. Download it from here. Users can contact me if interested in getting database files for species different from human.


July 31, 2013.

EricScript version 0.4.3 is now available. Download it from here
Updates: this version is now compatible with the new filesystem of Ensembl FTP. Previous versions are no longer usable to download databases from Ensembl.


June 10, 2013.

EricScript version 0.4.2 is now available. Download it from here
Updates:

• Revised demo command.
• Fixed small bugs.


April 27, 2013.

Users who have experienced problems in downloading ericscript database files due to connection issues (proxy, etc) can download the ready-to-use db data from here.


April 25, 2013.

EricScript version 0.4.1 is now available. Download it from here.
The new version requires bwa >= 0.7.4. This version introduces the following updates:

• BWA MEM as default aligner (greeeaat improvement in detecting spanning junction reads). Users can use bwa aln by setting --bwa_aln.
• Automatic update of indexes if a new version of bwa is detected. 
• Bugs fixed.

Make sure to re-build the indexes of your genome reference when a new version of bwa is installed.


March 19, 2013.

EricScript version 0.4.0 is now available. Download it from here.
It introduces the following major updates:

• Downloading of two or more species' database at time.
• Storage of databases in custom folder locations.
• Renewed EricScript Simulator with updated transcripts.
• Improved estimation of fusion junction sequences.
• Improved estimation of genomic breakpoints for fused genes.
• Improved user manual.
• Improved scoring accuracy*.

For users: comments and feedback are welcome!

* We improved scoring accuracy by training the adaboost classifier on further 10000 synthetic gene fusions, generated with high coverage (ranging from 50 to 500). The adaboost classifier has been trained by considering the scores (GJS, ES, US) and estimated gene fusion expression level.

Update (
March 20, 2013): some users get the following errors when running ericscript:

Use of uninitialized value in -d at ericscript-0.4.0/ericscript.pl line 172, <FILE> line 1.
Use of uninitialized value in mkdir at ericscript-0.4.0/ericscript.pl line 175, <FILE> line 1.
Use of uninitialized value in concatenation (.) or string at ericscript-0.4.0/ericscript.pl line 175, <FILE> line 1.

This appears when OUTPUTFOLDER ends with a slash ("/") character. You can replace this ericscript.pl file with the original one. Otherwise, in the current version this bug has been fixed.


February 8, 2013.

EricScript version 0.3.1beta is now available. It solves some bugs in building database and estimating genomic breakpoints for fused genes (thanks to Thomas Wu and Vladimir Kuryshev for the feedback). Download it from here.

Warning: the beta versions of EricScript don't support yet the simulator package.
  If you're interested in running the simulator for testing EricScript, please download ericscript-0.2.5.

We will release a new version of Eric in the next weeks that will include the following:

• Downloading of two or more organism's database at time.
• Storage of databases in custom folder locations.
• Renewed EricScript Simulator.



January 28, 2013.

EricScript version 0.3.0beta is now available. It introduces the following major updates:

• Compatibility with all the genomes available on the Ensembl Database.
• Easy way to retrieve data of the available genomes.
• Easy way to perform updates to your installed database.

The syntax on how to run ericscript is slighty changed since a bunch of new commands have been introduced. Read both the requirements and the getting started section to get more information.
The new version of EricScript is avaliable from here.

For users: I would be very grateful if you could give me some feedback!


November 20, 2012.

Ensembl Database is updated to version 69. To update your database, run:
 
ericscript.pl --checkdb


November 8, 2012.

In the recently published work "Reanalysis of RNA-Sequencing Data Reveals Several Additional Fusion Genes with Multiple Isoforms", Kangaspeska and colleagues discuss about the importance of refining bioinformatics pipeline in order to identify novel fusion genes that are present in already published data.
The data used by the authors are the same that we used in our paper to "validate" the EricScript pipeline. The results we obtained are reported in Supplemental File 1 and Supplemental File 2 of our paper. We are glad to observe that EricScript detected the majority of gene fusions (11/13) that they recently validated (as reported in Table 1 of their paper); moreover, the majority of these predicted fusions are called with an high score.
EricScript fails to detect two fusions that involve two genes (AC090627.1, AC099850.1) that are not present in the reference that we used for the identification of discordant reads; this results suggest us that we should take into account to revise our gene reference in order to detect more fusion events.

So.. great news for EricScript's users!


October 31, 2012.

EricScript version 0.2.5 is now available. It solves some small bugs and enables an easier debug process.
Download it from here.


October 24, 2012.

The paper describing the EricScript method has been published today in Bioinformatics! Read it here.
To receive announcements on EricScript updates or discuss EricScript usage with other users, join our google group.


October 11, 2012.

EricScript version 0.2.4 is now available. It solves some small bugs.
Download it from here.


October 9, 2012.

EricScript version 0.2.3 is now available. The module CalcStats is now able to process the output files of the following algorithms: EricScript, ChimeraScan, DeFuse, FusionMap and ShortFuse. Download it from here. Read more about the CalcStats module here.


October 4, 2012.

EricScript version 0.2.2 is now available. Now it includes the module CalcStats to calculate the statistical measures useful to evaluate the accuracy of gene fusion detection methods. Download it from here.


August 2, 2012.

EricScript version 0.2.1 is now available. Download it from here.
Major changes:

• Introducing EricScript simulator to generate synthetic datasets.
• Introducing the parameter ntrim to increase the sensitivity of EricScript for longer reads

Ensembl Database is updated to version 68.


May 28, 2012.

EricScript version 0.2.0 is now available. Download it from here.
Major changes:

• Introducing adaboost classifier as summarization score.
• Introducing a novel score for classifying fusion junctions (uniformity score, US).
• More accurate estimation of gene expression.
 

February 27, 2012.

Ensembl Database is updated to version 66. To update your database, run:
 
ericscript.pl --checkdb


February 17, 2012.

EricScript version 0.1.1 is now available. It fixes bugs in the output tab-delimited files.
Download it here.


November 18, 2011.


The first release of EricScript (0.1.0) is now available.