3.5 years ago by
The MACS documentation covers all of this in detail. Is linked from the tool page but also linked here:
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