Description

This track shows the meta summits from data processed from Theunissen et al. 2016, exploring the naive and primed human ES states.

These states have characteristic repeat expression patterns.

Two Chip-Seq assays were done, one for Kap1 and the other one for the H3K9me3 chromatin mark.

Display Conventions and Configuration

Meta summits are initially required to be above a threshold score of 100 (macs2 summit score).

Use in combination with the corresponding coverage and instance mapping tracks.

Methods

Using the Repeat Browser bed files (see "instance mapping tracks") we used macs2 to call peaks with the following settings

macs2 callpeak -f BED -t --keep-dup all --outdir data/macs2/ --nomodel --call-summits --extsize 30 -n

macs2 summits and peaks can be found in data/macs2 if you would like to load custom tracks with less stringently filtered meta summits.

References

Theunissen et al., Cell Stem Cell, 2016

Email max@soe.ucsc.edu or jferna10@ucsc.edu