Description

This track shows the meta summits from data processed from Schmittges et al. 2016 from the Hughes lab. ChIP-SEQ of many GFP tagged ZNFs in HEK293 cells. Not all proteins are human, and not all are KRAB-Zinc fingers proteins.

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

Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T et al. Multiparameter functional diversity of human C2H2 zinc finger proteins. Genome Res. 2016 Dec;26(12):1742-1752. PMID: 27852650; PMC: PMC5131825

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