Examples

PELT

Generate sample job (using N-myc hg18 promoter data)

Cotterman R, Jin VX, Krig SR, et al. N-myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Res. 2008 Dec 1;68(23):9654-62.
Raw data download:
hg18 promoter data (four .gff files, 21.3MB compressed, 249MB uncompressed): Nmyc_hg18.zip.
hg18 PELT results (file 10005402_ratio used)

Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ. A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res. 2006 Dec;16(12):1585-95. Epub 2006 Oct 19.
Raw data download:
hg17 tiling data (three .gff files, 12.9MB compressed, 104MB uncompressed): E2F.zip.
PELT results (all three .gff files used)

Bapat SA, Jin VX, Berry N, et al. Multivalent epigenetic marks confer microenvironment-responsive epigenetic plasticity to ovarian cancer cells. Epigenetics. 2010 Jul 14;5(8):716-729.
Raw data download (normalized Agilent data, two .gff files, hg18, run as Promoter, 4.9MB compressed, 38MB uncompressed): Bapat_et_al.zip
2D-H3Ac PELT results
2D-H3K9me2 PELT Results

BELT

Generate sample job (using ZNF263 replicate A data)

Frietze S, Lan X, Jin VX, Farnham PJ. Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem. 2010 Jan 8;285(2):1393-403. Epub 2009 Nov 2.
BELT analysis of ZNF263:
Replicate A raw data download (.bed format, 80MB compressed, 293MB uncompressed): ZNF263RepA.zip.
Replicate B raw data download (.bed format, 95.8MB compressed, 336MB uncompressed): ZNF263RepB.zip.
ZNF263 replicate A BELT results (includes enrichment and .WIG output)
ZNF263 replicate B BELT results (includes enrichment and .bedGraph output)

ENCODE Consortium PolII
Treatment file download (.bed format, 345MB compressed, 1010MB uncompressed): wgEncodeYaleChIPseqAlignmentsCombinedK562Pol2.tagAlign.zip.
Control file download (.bed format, 643MB compressed, 1.9GB uncompressed): K562_input_PolII.zip.
BELT results (includes .bedGraph output)

ENCODE Consortium H3K4me3
Treatment file download (.bed format, 659MB compressed, 2.1GB uncompressed): K562_H3K4me3_Broad_combinedRep.zip
Control file download (.bed format, 543MB compressed, 1.7GB uncompressed): K562_control_H3K4me3.zip
BELT results (target FDR: 10%, includes .WIG output)

Gan Q, et al. Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis.
Files are available at the GEO Omnibus, accession GSE19325.
DM3 BELT results (file GSM480156_dm3-S2-H3K4me3.bed used)