updated README.md

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.

README.md

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 # 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.
+<br />
+
+<b>May 2, 2020</b><br />
+
+The two options `--printdb` and `--downdb` often failed due to lack of `ftp` client in many environment. 
+
+