Schema for DeepER

Schema for DeepER - DeepER

Database: hg38 Primary Table: bigbed_DeepER_Human Data last updated: 2024-03-29
Big Bed File: /data01/chenjy/rloopbase/ucsc/gbdb/hg38/inhouse-tracks/DeepeR/DeepER.bb
Item Count: 79,626
Format description: Browser Extensible Data

field	example	description
`chrom`	chr1	Reference sequence chromosome or scaffold
`chromStart`	165975000	Start position in chromosome
`chromEnd`	165975210	End position in chromosome
`name`	.	Name of item.
`score`	0	Score (0-1000)
`strand`	-	+ or - for strand

Sample Rows

chrom	chromStart	chromEnd	name	strand
chr1	165975000	165975210	.	-
chr1	166166030	166166330	.	+
chr1	166166130	166166790	.	-
chr1	166166360	166166920	.	+
chr1	166248730	166249200	.	-
chr1	166335410	166335860	.	-
chr1	166342910	166343390	.	+
chr1	166839200	166839590	.	-
chr1	166839320	166839660	.	+
chr1	166839700	166840000	.	+

DeepER (DeepER_tracks) Track Description


	Description This track displays genome-wide R-loop-forming regions predicted by DeepER, a deep learning-enhanced tool built on a residual BiLSTM architecture. For each 5-kb genomic segment, DeepER computes base-level probabilities of R-loop formation, which are then processed using a sliding window (200 bp window size, 10 bp step size). Consecutive windows with an average probability = 0.95 (default cutoff) are merged to define high-confidence R-loop zones. The track provides both a continuous probability signal (available as a bigWig) and discrete R-loop zones, enabling users to assess predicted R-loop occupancy across the genome. This computational track complements experimental mapping data and offers a standardized view of sequence-intrinsic R-loop formation potential.