Usage: ericscript.pl [arguments] Optional arguments: -h, --help print help message -m, --man print complete documentation -v, --verbose use verbose output -name, --samplename what's the name of your sample? -o, --outputfolder where the results will be stored -minr, --minreads minimum reads to consider discordant alignments [3] -p, --nthreads number of threads for the bwa aln process [4] -ntrim trim PE reads from 1st base to $ntrim. Default is no trimming. Set ntrim=0 to don't trim reads. --MAPQ minimum value of mapping quality to consider discordant reads. For MAPQ 0 use a negative value [20] --remove remove all temporary files. --demo Run a demonstration of EricScript on simulated reads. --refid Genome reference identification. Run ericscript.pl --printdb to see available refid [homo_sapiens]. --bwa_aln Use BWA ALN instead of BWA MEM to search for discordant reads. Subcommands: --checkdb Check if your database is up-to-date, based on the latest Ensembl release. --simulator Generate synthetic gene fusions with the same recipe of the ericscript's paper --calcstats Calculate the statistics that we used in our paper to evaluate the performance of the algorithms. -------- arguments for databases subcommands (downdb, checkdb): --refid Genome reference identification. Run ericscript.pl --printdb to see available refid [homo_sapiens]. --printdb Print a list of available genomes and exit. --ensversion Download data of a specific Ensembl version (>= 70). Default is the latest one. ------- arguments for simulator: -o, --outputfolder where synthetic datasets will be stored [HOME/ericscript_simulator] -rl, --readlength length of synthetic reads [75] --refid Genome reference identification. Run ericscript.pl --printdb to see available refid [homo_sapiens]. -v, --verbose use verbose output --insize parameter of wgsym. Outer distance between the two ends [200] --sd_insize parameter of wgsym. Standard deviation [50] --ngenefusion The number of synthetic gene fusions per dataset? [50] --min_cov Minimum coverage to simulate [1] --max_cov Maximum coverage to simulate [50] --nsims The number of synthetic datasets to simulate [10] --be Use --be to generate Broken Exons (BE) data [no] --ie Use --ie to generate Intact Exons (IE) data [yes] --background_1 Fastq file (forward) for generating background reads. --background_2 Fastq file (reverse) for generating background reads. --nreads_background The number of reads to extract from background data [200e3]. ------- arguments for calcstats: -o, --outputfolder where statistics file will be stored [HOME/ericscript_calcstats] --resultsfolder path to folder containing algorithm results. --datafolder path to folder containing synthetic data generated by ericscript simulator. --algoname name of the algorithm that generated results. --dataset type of synthetic data to considered for calculating statistics. IE or BE? -rl, --readlength length of synthetic reads --normroc factor to normalize the score given by the algorithm. ericscript.pl automatically runs a pipeline to detect chimeric transcripts in paired-end RNA-seq samples. It is also able to generate datasets with synthetic gene fusions. More information about running EricScript Simulator and EricScript CalcStats can be found at http://ericscript.sourceforge.net Version: 0.5.5b Options: --help print a brief usage message and detailed explanation of options. --man print the complete manual of the program. --verbose use verbose output. --samplename Choose a name for your sample. Default is "MyEric" --outputfolder Folder that will contain all the results of the analysis. Default is YOUR_HOME/SAMPLENAME --minreads Minimum reads to consider discordant alignments. Default is 3 reads with minimum MAPQ. -ntrim trim PE reads from 1st base to $ntrim. Trimmed reads will be used only for the first alignment (identification of discordant reads). Setting ntrim to values lower than orginal read length allows EricScript to increase its sensitivity, especially when the length of reads is 75nt or 100 nt. Default is no trimming. Set ntrim=0 to don't trim reads. --nthreads Number of threads for the bwa aln process. --MAPQ minimum value of mapping quality to consider discordant reads. For MAPQ 0 use a negative value. Default is 20. --remove remove all temporary files. By default, all temporary files will be kept for user inspection, but this will easily clutter the directory. --checkdb Check if your database is up-to-date, based on the latest Ensembl release. --refid Genome reference identification. Run ericscript.pl --printdb to see available refid.[homo_sapiens] --ensversion Download data of a specific version of Ensembl. Default is downloading the latest version of Ensembl. Minimum supported version is 70. --printdb Print a list of available genomes and exit. --demo Run a demonstration of EricScript on simulated reads.