I have a ChIP-Seq data set with 4 IP and and Input samples as well as two IgG samples. When mapping the fastq samples (pair-end samples), I get very good results for the Input samples, but very bad results for the IgG samples and slightly better ones fro the IP samples:
Input1 | 93.61% Input2 | 97.41% Input3 | 97.75% Input4 | 94.08% IP1 | 54.41% IP2 | 83.16% IP3 | 75.63% IP4| 63.76% IP_IgG1 | 24.76% IP_IgG2 | 52.90%
I would like to understand why the IP and IgG reads weren't mapped as well as the Input. I have searched for contamination, but couldn't see any.
I would appreciate your suggestions as to how to pin-point this problem.