Galaxy |

MACS (version 1.0.1)

Experiment Name:

Paired End Sequencing:

ChIP-Seq Tag File:

ChIP-Seq Control File:

Effective genome size:

default: 2.7e+9

Tag size:

Band width:

Pvalue cutoff for peak detection:

default: 1e-5

Select the regions with MFOLD high-confidence enrichment ratio against background to build model:

Parse xls files into into distinct interval files:

Save shifted raw tag count at every bp into a wiggle file:

Use fixed background lambda as local lambda for every peak region:

up to 9X more time consuming

3 levels of regions around the peak region to calculate the maximum lambda as local lambda:

Build Model:

Diagnosis report:

up to 9X more time consuming

Perform the new peak detection method (futurefdr):

The default method only consider the peak location, 1k, 5k, and 10k regions in the control data; whereas the new future method also consider the 5k, 10k regions in treatment data to calculate local bias.

What it does

This tool allows ChIP-seq peak calling using MACS.

Depending upon selected options, 2 to 6 history items will be created; the first output will be a standard BED file and the last will be an HTML report containing links to download additional files generated by MACS. Up to two each of wig and interval files can be optionally created; the interval files are parsed from the xls output.

View the original MACS documentation: http://liulab.dfci.harvard.edu/MACS/00README.html.

Citation

For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

If you use this tool in Galaxy, please cite Blankenberg D, et al. In preparation.