Hello Yanina, According to the MACS documentation (also linked from the tool form): http://liulab.dfci.harvard.edu/MACS/00README.html The option controlling duplicates is (quote): --keep-dup=KEEPDUPLICATES It controls the MACS behavior towards duplicate tags at the exact same location -- the same coordination and the same strand. The default 'auto' option makes MACS calculate the maximum tags at the exact same location based on binomal distribution using 1e-5 as pvalue cutoff; and the 'all' option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location. Default: auto Galaxy implements this as the option on the tool form as "Pvalue cutoff for peak detection:" with "1e-05" as the default. Hopefully this helps! Jen Galaxy team On 8/31/12 8:38 AM, Yanina Bogliotti wrote:

Hi,

Does MACS remove duplicate reads automatically during the peak calling? I'm running controls for all the samples.

Thanks for your help,

Yanina

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