Putative human enhancers based on ReMap 2018 (hg38) (Q12326): Difference between revisions

To generate a collection of putative enhancer regions, we collected all transcription factor ChIP-seq peaks from ReMap 2018 (ref remap; http://remap.univ-amu.fr/storage/remap2018/hg38/MACS/remap2018_all_macs2_hg38_v1_2.bed.gz). We took the summit of all peaks and extended these 25 bp up- and downstream. Based on this file, we generated a coverage bedGraph using bedtools genomecov. We performed peak calling on this bedGraph file using bdgpeakcall from MACS2 2.2.7.1, with the following settings: l=50 and g=10. We performed the peak calling twice, setting c to 4 and 30, respectively. All peaks from c=30 were combined with all peaks of c=4 that did not overlap with the peaks of c=30. We then removed all regions on chrM and extended the summit of the peaks 100 bp up- and downstream to generate a final collection of 1,268,775 putative enhancers of 200 bp.