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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
-- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
