Question: Different results with manual MACS tool vs. workflow automated MACS tool for ChIP analysis
gravatar for christopher.paran
3.1 years ago by
United States
christopher.paran0 wrote:


i wanted to post about something i found out today working with the MACS tool (under NGS: peak calling) for ChIP analysis. i found that the MACS tool will run with the 'use fixed background lambda as local lambda for every peak region'  box invisibly checked when used as part of an automated workflow. you will see an error message in the MACS html output file that says !!!! DYNAMIC LAMBDA IS DISABLED !!!!. the results appear incorrect as well.

this is a bug, but you can get around it by checking this option box in the saved workflow - this has the effect of running as unchecked.

i can't find the bug report button, so i haven't reported it as a bug, but it would be good to fix probably. perhaps there are other invisibly checked options with this tool as well that i haven't noticed.

cheers, chris

p.s. i am using the online interface for Galaxy at

workflow lambda macs chip-seq • 845 views
ADD COMMENTlink modified 3.1 years ago by Dannon Baker3.7k • written 3.1 years ago by christopher.paran0
gravatar for Dannon Baker
3.1 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

Hi Chris, thanks for noticing this and taking the time to report it!

This was an unfortunate bug that existed briefly on the server but has since been fixed and Galaxy has been updated.  If you run your analysis again, you should observe the intended parameter usage.


ADD COMMENTlink written 3.1 years ago by Dannon Baker3.7k
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