Need help with "MACS" tool

Question: Need help with "MACS" tool

4.2 years ago by

zhhxu9 • 0

Canada

zhhxu9 • 0 wrote:

Hi everyone,

I don't quite understand the meaning of the parameters of this program.

1. What is the effective genome size for Arabidopsis thaliana?

2. What do tag size and band width mean?

3. Usually how to setup Pvalue cutoff for peak detection?

4. How to choose 3 levels of regions around the peak region to calculate the maximum lambda as local lambda?

I appreciate for kind help!

Zhenhua

Tool name: MACS
Tool version: 1.0.1
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/macs

macs • 1.6k views

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modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by zhhxu9 • 0

4.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Zhenhua,

The MACS documentation covers all of this in detail. Is linked from the tool page but also linked here:
http://liulab.dfci.harvard.edu/MACS/00README.html

Here are some brief answers:

1. What is the effective genome size for Arabidopsis thaliana?

Size of the reference genome in bases. It depends which version you are using. This is generally
available from the original data source (source/common acronym a genomes in included in the full
genome name description) or from where you obtained a Custom Reference Genome (if used).

2. What do tag size and band width mean?

Tag size is the length of the input mapped reads. Band width is the size of the peak regions.

3. Usually how to setup Pvalue cutoff for peak detection?

The default is generally used, but you can experiment with this and review prior discussion at
the MACS google group, seqanswers.com, and biostars.org plus publications that utilize this tool.

4. How to choose 3 levels of regions around the peak region to calculate the maximum lambda as local lambda?

There are defaults set, but these again can be modified to suit. The same resources as for #3 are good
places to research what others are using doing research similar to yours. ChIP-Seq protocols included
in ENCODE pipelines at UCSC could also be a resource, but this specific tool is will not be included in all.

Hopefully this helps! Jen, Galaxy team

ADD COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks a lot.

ADD REPLY • link written 4.2 years ago by zhhxu9 • 0

What would the actual effective genome size of A. thaliana would be? Thanks!

ADD REPLY • link written 9 months ago by jenyka_dm • 10

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