Question: Macs- Duplicate Reads Removal
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gravatar for Yanina Bogliotti
5.9 years ago by
Yanina Bogliotti20 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
macs • 1.5k views
ADD COMMENTlink modified 5.9 years ago by Jennifer Hillman Jackson25k • written 5.9 years ago by Yanina Bogliotti20
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gravatar for Jennifer Hillman Jackson
5.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENTlink written 5.9 years ago by Jennifer Hillman Jackson25k
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