Why? I am trying to use MapSplice to find fusion now. I used theirs because they are conservative and every fusion must be supported by multiple reads with different starting points.
How? They support both parameters in command line or parameters in a configure file. And for pair-end data, the 2 parts of reads from the same pair must be stored in a separate file and in the configure file they must in a format like: s_1_1_seq.txt,s_1_2_seq.txt,s_2_1_seq.txt,s_2_2_seq.txt . with no space in between the file names, just coma.
Remember! If no file path are given in the configure file, MapSplice should be running in the directory that have the seq data (I am too careless).
What's going on? MapSplice is still check my reads format.
