Difference between revisions of "Run MACS 1.3.7 on ChiP-Seq (analysis)"

Revision as of 16:05, 4 April 2013

MACS (Model-based analysis of ChiP-Seq data) empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites.

Parameters:

• Track – Filtering track
• Control track – Control track (can be omitted)
• Use fixed lambda – Use fixed background lambda as local lambda for every peak region
• Lambda set – Three levels of nearby region in basepairs to calculate dynamic lambda
  • lambda 1 – lambda 1
  • lambda 2 – lambda 2
  • lambda 3 – lambda 3
• No model – Do not build the shifting model. In this mode shift size parameter is used.
• Shift size – The arbitrary shift size in bp. Used in no-model mode.
• Band width – Band width
• Genome size – Effective genome size
• Enrichment ratio – High-confidence enrichment ratio against background
• Tag size – Tag size
• P-value – P-value cutoff for peak detection
• Future FDR – Adopt the new peak detection method as new standard. The default method only considers the peak location in the 1k, 5k, or 10kb regions of the control data. In contrast, the new method also considers the 5k or 10k regions of the test data to calculate the local bias.
• Output name – Output name

More about MACS: http://liulab.dfci.harvard.edu/MACS/

Reference: Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137