Currently sRNAbench and sRNAde can be downloaded as standalone versions
sRNAbench and sRNAde are implemented in JAVA and need apart from a JRE the following third party software that needs to be installed and placed in the PATH first.
- Vienna RNA package for RNA Secondary Structure Prediction and Comparison Vienna package 2. sRNAbench will only work with Vienna 2.0 or higher!
- Bowtie – An ultra-fast memory-efficient short read aligner (Bowtie). sRNAbench will only work with Bowtie1 but not Bowtie2.
- For the differential expression program sRNAde: edgeR package , DEseq , NOISeq  (R packages) and The Apache Commons Mathematics Library
- SRA tool kit: only if the user wants to use data from SRA as input files as those need to be converted to fastq first.
sRNAbench and sRNAde rely on a local database where most of the library files, genome sequences, Rscripts and Bowtie indexes need to be stored. The database can have any arbitrary name and the easiest way to generate it is by means of the “start-up” DB following the next steps:
- Download the “start-up” database: sRNAtoolboxDB. Please note that this does not generate a full database, i.e. it includes only microRNAs for Human, human herpesvirus type 8 (HHV-8) and Epstein-Barr virus (EBV). To populate the database, please see below.
- Extract it to the directory of your choice: tar xvzf sRNAtoolboxDB.tgz . We recommend to use /opt/sRNAtoolboxDB (All programs take this directory as default value)
- Download the most recent version and replace the sRNAbench.jar and sRNAde.jar files form the database: sRNAbench.jar && sRNAde.jar
After extracting the database, you should see the following folders:
- libs: The default location for all sequence libraries except the genome sequences
- index: This folder contains the Bowtie indexes of the genome sequences
- seqOBJ: This folder contains the prepared genome sequences in order to access them rapidly (the files can be generated by means of the makeSeqObj program).
- exec: the programs, i.e. jar and other executable files
out: The default output folder. This directory is always used if the output= parameter is omitted