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Old 05-24-2011, 07:09 PM   #1

Join Date: Sep 2009
Posts: 74
Default technical replicates uncorrelate with each other


I do chip-seq aganist gammaH2AX, one of histone modification, which indicates DNA damage and repair.
At the beginning I just have about 7M reads (chip) and 4.7M reads (input) and using SICER to get enrishment profile on genome (human hg18).
Then I send the exactly the same sample to sequencing (chip sample) and getting 11M reads and I don`t sequence input sample this time and use the same input to get enrishment profile.
My question is I find those two profiles have large differences.

can you give me some advice?
thanks in advance
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