https://github.com/databio/ericscript
Chimeric transcript discovery
https://github.com/databio/ericscript
Last synced: about 1 year ago
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Chimeric transcript discovery
- Host: GitHub
- URL: https://github.com/databio/ericscript
- Owner: databio
- License: gpl-3.0
- Created: 2018-05-21T12:00:46.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2018-05-25T15:52:32.000Z (about 8 years ago)
- Last Synced: 2025-03-26T13:11:22.356Z (over 1 year ago)
- Language: R
- Size: 1.14 MB
- Stars: 8
- Watchers: 9
- Forks: 2
- Open Issues: 5
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
## 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.