diff --git a/README b/README new file mode 100644 index 0000000..18fb70e --- /dev/null +++ b/README @@ -0,0 +1,67 @@ +# 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. diff --git a/README.md b/README.md index 8eccdb5..d5aabdc 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,14 @@ # EricScript + +`EricScript` was developed at https://sites.google.com/site/bioericscript/ +However maintaince was stopped after the last update v0.5.5 (April 2016) + +In this project, `EricScript` will be maintained to work. +
+ +May 2, 2020
+ +The two options `--printdb` and `--downdb` often failed due to lack of `ftp` client in many environment. + +