In order to run the Fusion_finder script the following is required.
1) requires samtools/0.1.16
2) requires a folder structure including a CIS LOC and RESULTS folders.
(included in the zipped up directory)
3) requires the input.txt file which includes in tab delimited text file.
input.txt
/home/largaesp/shared/RNASEQ/OSX_mice/Largaespada_Project_073/part1/bam/OSX109_sorted.bam	O109	loc_SB
a) the path to and name of a bam file.
b) human readable short name of the bam file.
c) the location of the the file to tell the software what region of the genome to look for fusions in in the example case this value is 'LOC_SB'
loc_SB
chrSB:0-200	chrSB:0-200
chrSB:450-650	chrSB:450-650
chrSB:900-1100	chrSB:900-1100
chrSB:1400-1600	chrSB:1400-1600
chrSB:2000-2200	chrSB:2000-2200

run the script by entering the following command line 
perl FUSION_FINDER.pl
will generate the file 
Results/RNA_insertion_O109.loc_SB.txt
and will generate the summary file fus.txt


To modify the script to examine different bam files modify input.txt to include the location of new bam files. Multiple lines can be added.

To modify the location to examine for fusions add/modify lines in the loc_SB files.


Happy hunting!

 
