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

Database: dm6 Primary Table: H3K9me2_PePr Data last updated: 2016-01-26
Big Bed File: /gbdb/dm6/bbi/H3K9me2_PePr.bb
Item Count: 10,807
Format description: Format used for the output of the PePr peak caller

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15826980	Start position in chromosome
`chromEnd`	15828180	End position in chromosome
`name`	H3K9me2_PePr_7844	Short Name of item
`score`	72	Score from 0-1000
`strand`	+	+ or -
`pValue`	9.35408	Statistical significance of signal value (-log10).
`qValue`	7.23607	Statistical significance with multiple-test correction applied (FDR).

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	pValue	qValue
chr2L	15826980	15828180	H3K9me2_PePr_7844	72	+	9.35408	7.23607
chr2L	15828810	15829110	H3K9me2_PePr_7845	71	+	9.26438	7.15576
chr2L	16141290	16141380	H3K9me2_PePr_7846	58	+	7.74773	5.82060
chr2L	16512360	16512600	H3K9me2_PePr_7847	57	+	7.68458	5.76646
chr2L	16512750	16512870	H3K9me2_PePr_7848	41	+	5.68636	4.17083
chr2L	16513620	16515120	H3K9me2_PePr_7849	62	+	8.24511	6.25248
chr2L	16515240	16518420	H3K9me2_PePr_7850	76	+	9.83003	7.66553
chr2L	16518540	16518630	H3K9me2_PePr_7851	38	+	5.22044	3.83207
chr2L	16558560	16558650	H3K9me2_PePr_7852	37	+	5.17521	3.79956
chr2L	17145120	17145210	H3K9me2_PePr_7853	42	+	5.80733	4.26029

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