DROMPA - Peak-calling and Visualization Tool for Multiple ChIP-seq Data
DROMPA (DRaw and Observe Multiple enrichment Profiles and Annotation) is a program for
user-friendly and flexible ChIP-seq pipelining. DROMPA can be used for quality check, PCRbias
filtering, normalization, peak calling, visualization and other multiple analyses of ChIP-seq
data. DROMPA is specially designed so that it is easy to handle, and for users without a strong
Source code and the manual of DROMPA3 are available on GitHub repository
DROMPA can include several kinds of genomic annotations downloaded from public database listed below.
The latest annotation data files can be downloaded from original websites.
The same genome build (e.g. hg19) should be used for genome sequence and annotation data.
- RefSeq Gene Data ("refFlat.txt" downloaded from UCSC genome browser)
- Ensembl Gene Data (obtained from BioMart at the Ensembl website and the format was modified)
- RepBase Repeat Data ("Repbase.txt" downloaded from UCSC genome browser)
- GC Contents Data (per 500k bp) (convert from fasta files by "GCcount.pl" in scripts directory in DROMPA)
- Gene density Data (per 500k bp)
- Mappability Data
- S. cerevisiae
- S. pombe
Copyright © 2012-2018 Ryuichiro Nakato