Different results with manual MACS tool vs. workflow automated MACS tool for ChIP analysis
1
0
Entering edit mode
6.9 years ago

hi,

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

ChIP-Seq MACS LAMBDA workflow Forum • 3.0k views
ADD COMMENT
0
Entering edit mode

Can you be more specific about the "Workflow automated MACS tool" - what implementation are you working with? I'm aware of MACS as a standalone python program, but you mention radio buttons and html with no other identifying info. Suite name? URL?

ADD REPLY
0
Entering edit mode

I'm guessing that this is a galaxy workflow.

ADD REPLY
0
Entering edit mode

right, sorry for not mentioning it in the original post. i was using the online interface Galaxyproject.org

ADD REPLY
0
Entering edit mode

Guys is the question frames correctly. when I say yes to use local lamda it gives me a message saying dyanamic lambda is disabled. When I run the workflow clicking on No to use local lambda. I dont get the error.

Please can somebody point out what is lamda and why is it importantto use or not to use.

ADD REPLY
1
Entering edit mode
6.9 years ago

Perhaps this should be posted on the Galaxy Biostar: https://biostar.usegalaxy.org/

ADD COMMENT
0
Entering edit mode

good point, I didn't know they were different forums. I've created a new post in that forum...thanks!

ADD REPLY

Login before adding your answer.

Traffic: 2299 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6