Schema for PePr Histone Modifications Peaks - ChIP-Seq Peaks Identified by PePr

Database: dm6 Primary Table: H3K27me3_PePr Data last updated: 2016-01-26
Big Bed File: /gbdb/dm6/bbi/H3K27me3_PePr.bb
Item Count: 5,602
Format description: Format used for the output of the PePr peak caller

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	16412070	Start position in chromosome
`chromEnd`	16412160	End position in chromosome
`name`	H3K27me3_PePr_4403	Short Name of item
`score`	37	Score from 0-1000
`strand`	+	+ or -
`pValue`	5.27787	Statistical significance of signal value (-log10).
`qValue`	3.77473	Statistical significance with multiple-test correction applied (FDR).

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	pValue	qValue
chr2L	16412070	16412160	H3K27me3_PePr_4403	37	+	5.27787	3.77473
chr2L	16416000	16416210	H3K27me3_PePr_4404	47	+	6.49097	4.76679
chr2L	16416990	16417140	H3K27me3_PePr_4405	43	+	5.92112	4.30290
chr2L	16418430	16418760	H3K27me3_PePr_4406	57	+	7.72372	5.75109
chr2L	16419180	16419660	H3K27me3_PePr_4407	68	+	9.15573	6.88711
chr2L	16419990	16421550	H3K27me3_PePr_4408	71	+	9.42232	7.10047
chr2L	16421760	16422720	H3K27me3_PePr_4409	91	+	11.99886	9.19060
chr2L	16423080	16423710	H3K27me3_PePr_4410	88	+	11.60560	8.86362
chr2L	16424070	16425150	H3K27me3_PePr_4411	75	+	9.92579	7.50345
chr2L	16426230	16426980	H3K27me3_PePr_4412	69	+	9.28970	6.99375

PePr Histone Modifications Peaks (PePr_peaks) Track Description


	Description ChIP-Seq data for H3K4me2, H3K9me2, and H3K27me3 were analyzed using PePr in order to identify regions in the D. melanogaster genome that are enriched for these histone modifications. Reads from the two replicates for each histone modification were provided to PePr in a single run. Regions enriched in H3K4me2 were identified using PePr with the following parameters: `--peaktype=sharp --remove_artefacts` Regions enriched in H3K9me2 and H3K27me3 were identified using PePr with the following parameters: `--peaktype=broad --remove_artefacts` References Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA. PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics. 2014 Sep 15;30(18):2568-75.

Description

References