The major issue of The RNAseq data from patient derived xenofraft samples (i.e, human tissue that is engrafted in mouse) is mouse contamination. This program removes mouse reads and ambiguous reads from the aligned SAM files. This program was written for the SAM files aligned with novoaligner.
The program take two input arguments ( human and mouse sam file).
The program has three outputs :
1.Human_unique reads 2. Human_hybrid reads ( comes from the human sam file) 3. Mouse_hybrid reads ( comes from the mouse sam file)