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CCAT specifications


Unique identifier OMICS_00428
Alternative name Control based ChIP-Seq Analysis Tools
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes




No version available

Publication for Control based ChIP-Seq Analysis Tools

CCAT citations


Integrated analysis of hematopoietic differentiation outcomes and molecular characterization reveals unbiased differentiation capacity and minor transcriptional memory in HPC/HSC iPSCs

PMCID: 5259886
PMID: 28114969
DOI: 10.1186/s13287-016-0466-1

[…] s mapped) as previously described []. MACS (v1.4.1) software was used to identify regions enriched for DNA methylation (peaks) using the default parameters []; the cutoff P value was set at 1 × 10-5. CCAT (v3.0) software was used to identify histone modification-enriched regions (peaks) using the parameters as previously reported []; the FDR cutoff was set at 0.05.For the transcriptional memory an […]


Identifying peaks in * seq data using shape information

BMC Bioinformatics
PMCID: 4905608
PMID: 27295177
DOI: 10.1186/s12859-016-1042-5

[…] ferred to as peak calling. Fig. 1Many different approaches to peak calling have been developed. The density of the ChIP signal can be analysed directly (Findpeaks []) or compared to a control signal (CCAT [], CisGenome [], Erange [], PeakSeq []). Signal processing approaches including Gaussian Kernel Density Estimation (FSeq [], QuEST []), Hotelling filters (DFilter []) and wavelets [] have also b […]


Recent advances in ChIP seq analysis: from quality management to whole genome annotation

Brief Bioinform
PMCID: 5444249
PMID: 26979602
DOI: 10.1093/bib/bbw023

[…] [] for a detailed discussion regarding control samples.Early programs adopted the Poisson model, which assumes that the background reads are uniformly distributed along the genome (e.g. SICER [] and CCAT []). However, a greater variation in the read distribution than allowed by the Poisson model is typically experimentally observed, and the negative binomial model that is an extension of the Pois […]


Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns

PMCID: 5068885
PMID: 26784972
DOI: 10.1038/tp.2015.214

[…] r of epigenetic control, the post-translational modification of histones. Using the histone mark map for human adult brain inferior temporal lobe available from the ROADMAP project (GSE17312) and the CCAT peak caller, we observed that >95% of the DMRs co-localized with euchromatin markers such as H3K4me1, H3K4me3, H3K36me3 and H3K27ac (OR=5.7; bootstrap P<0.001), while heterochromatin regions rema […]


Different promoter affinities account for specificity in MYC dependent gene regulation

PMCID: 4963202
PMID: 27460974
DOI: 10.7554/eLife.15161.036

[…] ed with MACS v.1.4.2 (parameters: --keep-dup 3, variable p-value cut-off), SICER v.1.1 (parameters: redundancy 1, window 200, fragment size 90, effective genome fraction 0.74, gap 0, FDR 0.01) () and CCAT v.3.0 (parameters: default for transcription factors) (). Overlapping peaks were determined with the 'intersectBed' function from BEDTools v.2.17.0 (). Promoter regions are defined as –1.5 kb to […]


Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome

Front Genet
PMCID: 4664705
PMID: 26648976
DOI: 10.3389/fgene.2015.00339

[…] apped with Bowtie version 0.12.7 to the female human genome (UCSC hg19). Only uniquely mapping reads were used for further analysis; clonal reads were removed. Initial peak calling was performed with CCAT version 3.0 (Xu et al., ) with the following parameters: fragmentSize = 150, slidingWinSize = 500, movingStep = 50, isStrandSensitiveMode = 0, minCount = 4, outputNum = 10000, randomSeed = 123456 […]


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CCAT institution(s)
Computational & Mathematical Biology Group, Genome Institute of Singapore, Singapore; School of Computer Engineering, Nanyang Technological University, Singapore; Genome Technology & Biology Group, Genome Institute of Singapore, Singapore; School of Computing, National University of Singapore, Singapore; School of Biological Science, Nanyang Technological University, Singapore

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