Question: information about MACS analysis in Galaxy
gravatar for pabla86
3.7 years ago by
pabla860 wrote:

I have used MACS v1 in Galaxy to call peaks. I know that MACS automatically removes duplicate reads (or most of them) during peak calling analysis, and I would like to ask you if in Galaxy it is configured to do this, or if I need to do it explicitly. In this case, should I use the "NGS: Picard (beta) -> Mark Duplicate reads" option, right?

Many thanks,



peak calling • 771 views
ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by pabla860
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello Paola,

As far as I know, you will generally not want to do any steps between mapping (BWA or such) and running MACS to avoid introducing any bias. 

MACS is implemented with most of the default settings. The exact setting can be reviewed in the Tool Shed repository (to view this, on most tool forms use the upper right corner "Options" menu to "See in Tool Shed").

Once you run MACS, you will understand more. The command-line is reported on the "info" page and unique/total counts are in the Galaxy output report header, like this:

# unique tags in treatment: 479180

# total tags in treatment: 487929

Best, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
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