Name | Modified | Size | Downloads / Week |
---|---|---|---|
ericscript-0.5.5.tar.bz2 | 2016-05-03 | 510.9 kB | |
ericscript-0.5.4.tar.bz2 | 2016-03-02 | 510.6 kB | |
README | 2016-02-25 | 3.0 kB | |
ericscript-0.5.3.tar.bz2 | 2016-02-25 | 510.8 kB | |
ericscript-0.5.2.tar.bz2 | 2015-10-06 | 510.4 kB | |
ericscript-0.5.1.tar.bz2 | 2015-06-12 | 510.5 kB | |
ericscript-0.5.0.tar.bz2 | 2014-08-26 | 503.5 kB | |
ericscript-0.4.3.tar.bz2 | 2014-03-10 | 502.7 kB | |
ericscript-0.4.2.tar.bz2 | 2013-06-10 | 502.6 kB | |
ericscript-0.4.1.tar.bz2 | 2013-04-25 | 508.2 kB | |
ericscript-0.4.0.tar.bz2 | 2013-03-20 | 502.1 kB | |
ericscript-0.3.1beta.tar.bz2 | 2013-02-09 | 445.1 kB | |
ericscript-0.3.0beta.tar.bz2 | 2013-01-29 | 444.5 kB | |
ericscript-0.2.5.tar.bz2 | 2012-10-31 | 440.8 kB | |
ericscript-0.2.4.tar.bz2 | 2012-10-11 | 441.0 kB | |
ericscript-0.2.3.tar.bz2 | 2012-10-09 | 441.3 kB | |
ericscript-0.2.2.tar.bz2 | 2012-10-04 | 440.8 kB | |
ericscript-0.2.1.tar.bz2 | 2012-08-02 | 353.8 kB | |
ericscript-0.2.0.tar.bz2 | 2012-05-28 | 372.7 kB | |
ericscript-0.1.1.tar.bz2 | 2012-02-27 | 275.2 kB | |
ericscript-0.1.0.tar.bz2 | 2011-11-21 | 275.8 kB | |
Totals: 21 Items | 9.0 MB | 0 |
# 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.