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

Database: dm6 Primary Table: H3K4me2_PePr Data last updated: 2016-01-26
Big Bed File: /gbdb/dm6/bbi/H3K4me2_PePr.bb
Item Count: 18,213
Format description: Format used for the output of the PePr peak caller

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15731100	Start position in chromosome
`chromEnd`	15731310	End position in chromosome
`name`	H3K4me2_PePr_13969	Short Name of item
`score`	64	Score from 0-1000
`strand`	+	+ or -
`pValue`	7.52044	Statistical significance of signal value (-log10).
`qValue`	6.45242	Statistical significance with multiple-test correction applied (FDR).

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	pValue	qValue
chr2L	15731100	15731310	H3K4me2_PePr_13969	64	+	7.52044	6.45242
chr2L	15731820	15732030	H3K4me2_PePr_13970	45	+	5.50772	4.58377
chr2L	15744210	15744300	H3K4me2_PePr_13971	45	+	5.49376	4.57085
chr2L	15744480	15744870	H3K4me2_PePr_13972	64	+	7.48789	6.42205
chr2L	15745110	15745200	H3K4me2_PePr_13973	50	+	6.03689	5.07271
chr2L	15745230	15745440	H3K4me2_PePr_13974	51	+	6.16018	5.18698
chr2L	15745800	15746880	H3K4me2_PePr_13975	148	+	16.80982	14.86277
chr2L	15746940	15747000	H3K4me2_PePr_13976	43	+	5.22390	4.32312
chr2L	15747150	15747210	H3K4me2_PePr_13977	41	+	5.04755	4.16150
chr2L	15747240	15748170	H3K4me2_PePr_13978	166	+	19.01490	16.67455

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