DGE-EM README Installation: ------------ 1. Create a DGE-EM directory and download the installer jar file from http://dna.engr.uconn.edu/software/DGE-EM/dge-em-1.0.0-install.jar 2.1. With graphical interface: on most platforms double clicking on the icon will start the installer, otherwise type java -jar dge-em-1.0.0-install.jar at the command line 2.2 Text mode: if no graphical user interface is available, type java -jar dge-em-1.0.0-install.jar -console at the command line and follow the instructions 3. [Optional] On Windows you might want to add the DGE-EM installation directory to the path, such that you can invoke dge-em from any location. On Unix you can obtain a similar effect by creating a symbolic link to dge-em in /usr/local/bin. Running DGE-EM: -------------- DGE-EM takes as input a set of known isoforms in GTF format, a fasta file with the mRNA sequences of the known isoforms and one or more fastq files containing the DGE tags. If you don't have the mRNA sequences but have the GTF and the genome, you can use the extract-isoform-sequences-from-genome script included in this installation to extract and optionally add polyA tails to the isoform sequences. The output consists of two files: one for isoform frequencies and one for gene frequencies. Each line in these files is a pair of name and frequency. By default, these files are called dge.iso_estimates and dge.gene_estimates, but you can change the 'dge' prefix by using the -o option (see below). You can run DGE-Em from the command line as follows: dge-em [options]* file1.fastq file2.fastq ... Option Description ------ ----------- -G, --GTF Known genes and isoforms in GTF format -c, --gene-clusters Override isoform to gene mapping defined in the GTF file with a mapping taken from the given file. The format of each line in the file is "isoform gene". -e Enzime cutting patterns (comma separated, no spaces - e.g. CATG) -h, --help Show help -m Isoform MRNA sequences in 5' to 3' orientation --max-mismatches Maximum number of mismatched allowed for a tag (default 1). -o Output files prefix (default 'dge') --prepend-enzyme Use this flag if the recognition site for the enzyme is not included in the tags Source Code: ------------ The source code can be found in the src directory under the installation path. Revision history ---------------- Version 1.0.0 (2/22/11) - first public release Contact ------- For questions or suggestions regarding DGE-EM you can contact: Marius Nicolae (man09004@engr.uconn.edu) Ion Mandoiu (ion@engr.uconn.edu)