Installation

Installing Fusim

Fusim is written in Java and requires a working Java runtime version 1.6 or greater

1. Download Fusim
2. Unpack the .tar.gz or .zip file as follows:

   $ unzip fusim-X.X.X.zip
   $ cd fusim-X.X.X
   

3. Run Fusim:

   $ java -jar fusim.jar --help
   
   usage: fusim --gene-model=refFlat.txt [options]
   

Download gene model from UCSC

1. Download UCSC RefFlat GenePred data:

   $ wget -O refFlat.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt
   $ gunzip refFlat.txt.gz
   

Index reference genome file

1. Download genome reference from UCSC:

   $ wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

2. Extract and build one single fasta file:

   $ tar -xzf chromFa.tar.gz
   $ cat chr*.fa > hg19.fa

3. Index using samtools:

   $ samtools faidx hg19.fa