Required:

1. Hg19 genome sequences downloaded from UCSC
2. cdna sequences from ENSEMBL, RefSeq and UCSC knownGene
3. gtf file from Ensembl
4. rrna sequences

You may prepare data by yourself or download from www.utdallas.edu/~yongjin/asmFusion_data.tar.gz

5. softwares, bowtie, samtools, cdbyank, cdbfasta, gfClient, gfServer, Trinity and bioperl

All of them except bioperl are included in the asmFusion folder.


Input: data folder and read length
Data files are end_1.txt and end_2.txt. You may modify step_1.pl for your data.

Output is in the subfolder of data folder

Three steps for asmFusion:

Step 1 is mapping. Input is the data folder and read length. 
Step 2 is for fusion detection.
Step 3 is for remove. 

Three main programs, step_1.pl, step_2.pl and step_3.pl. In the head of each file, you will find configure information. You may change it according to your data.

Before running step_2.pl, you need to setup the gfServer 'gfServer start localhost 6666 -stepSize=5 -repMatch=4096 /pathTo/Hg19.2bit'.

In step_2.pl, some jobs will be submitted to cluster. Please run step_3.pl until all the jobs in step 2 are finished. 

Contact: yongjin.li@gmail.com.
