Question: Need help with "MACS" tool
0
gravatar for zhhxu9
4.0 years ago by
zhhxu90
Canada
zhhxu90 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 • 1.5k views
ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by zhhxu90
0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k

Thanks a lot.

ADD REPLYlink written 4.0 years ago by zhhxu90

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

ADD REPLYlink written 6 months ago by jenyka_dm10
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