CAGE peaks (hg38 v3)

CAGE peaks === This folder contains the CAGE peaks defined in the FANTOM5 project as a robust set, where genomic coordinates originally defined on hg19 are lifted to hg38 by liftOver tool. By following the update, their annotations are also updated - see “CAGE_peaks_annotation” directory in the parent directory. - Inquiries: [e-mail] - Update: 2015-09-18 initial release 2016-07-22 ver.2 release 2017-04-14 ver.3 release Data files --- - hg38_liftover_CAGE_peaks_phase1and2.bed.gz : all lifted-over CAGE peaks using UCSC Lift-over - hg38_fair_CAGE_peaks_phase1and2.bed : fairly remapped CAGE peaks. - hg38_problematic_CAGE_peaks_phase1and2.bed : problematic CAGE peaks that were filtered out by QC - hg38_new_CAGE_peaks_phase1and2.bed : newly identified CAGE peaks in hg38 DPI clustering - hg19_droppped_CAGE_peaks_phase1and2.bed : unmapped CAGE peaks (in hg19 coordination) Description of the columns in CAGE peaks coordinates files --- This is baed on BED9 format, where the thickStart and thickEnd position represent representative TSS positions. (https://genome.ucsc.edu/FAQ/FAQformat.html#format1) - chromosome - start of CAGE peak region - end of CAGE peak region - name (ID) of the CAGE peak - score - strand of the CAGE peak - start of the representative TSS position - end of the representative TSS position (Note: end is always start+1) - rgb string for color coding (plus or minus strand only)