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Old 03-06-2014, 10:46 AM   #1
Location: UK

Join Date: Nov 2010
Posts: 49
Default ChIPseq - how to qc the results ?

I just received our first chipseq sequencing results. I tried to use 2 packages to get the interesting peaks (MACS and Homer). Homer produces various qc graphs that seem to be fine, quality-wise. as expected, our igg control has random tags all over. my problem is, that our positive fraction (pulldown of antibody specific for our DNA-methyltransferase of interest ) doesnt seem that much "enriched". due to various problems (to high phix spike on top of lower clustering), we got ~5mln aligned reads/sample. that sounds about right to see a lot of peaks. How to test that actually somebody got a successfull IP ? I saw some of the RT-PCR fold changes, but they were not that impressive (eg 2-5fold, I havent seen the raw RTpcr data, eg fold changes obtained on cT's above 30'ish would be questionable, right). What to look for in terms of obvious IP/lib prep problems ?
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