ChIP-seq Input correlation
Hello Everyone
I have done multiBamSummary on my ChIP-seq data, and i found that the data has correlation with my Input is 0.98 which is almost similar, What i mean is my treatment data file and Input file is showing correlation 0.98
My question is should i go for downstream analysis or not ?
Thanks
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chaudharyc61 •
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Can you show a screenshot from a genome browser. You can create normalized browser tracks with e.g.
bamCoveragein deeptools using--normalizeUsing CPM. If this correlation is true it might be that your IP was insufficient and you basically did not ChIP anything beyond unspecific bindings. Also please give some details on what you ChIPed.