Description

This track shows the meta summits from a large scale ChIP-SEQ study described in Tsankov et al., "Transcription factor binding dynamics during human ES cell differentiation", Nature 2015. In this work, the authors performed ~38 ChIP-SEQ of transcription factors in stem cells at different stages of differentiation (pluripotent state, endodem, mesoendoderm, etc).

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

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