I have four methylation samples (MeDIP-seq) of two related plant species, testing methylation in case of saline stress. details are as follows:
Sample 1: Species 1 no stress
Sample 2: Species 1 with saline stress
Sample 3: Species 2 no stress
Sample 4: Species 2 with saline stress
Now when I map these reads to the genome (using BWA) I get 95 % mapping for Sample 1 and 3 while Sample 2 and 4 shows 23 % mapping. I am not able to understand the reason. All samples have ~25 mill reads and the sample extraction and quality of reads really is good !! Has anyone faced this problem ?? What can be the cause ??