DROMPA - Peak-calling and Visualization Tool for Multiple ChIP-seq Data

Overview

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 bioinformatics background.

DROMPA3

Source code and the manual of DROMPA3 are available on GitHub repository.

Older version

• Source code archive
• Manual Page for DROMPA2
• Manual Page for DROMPA1

Annotation data

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.
Note: 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)
  • (hg18, hg19, mm9, mm10)
• Ensembl Gene Data (obtained from BioMart at the Ensembl website and the format was modified)
  • (protein-coding only) (hg18, hg19, mm9)
  • (all genes) (hg18, hg19, mm9)
• RepBase Repeat Data ("Repbase.txt" downloaded from UCSC genome browser)
  • (hg18, hg19, mm9)
• GC Contents Data (per 500k bp) (convert from fasta files by "GCcount.pl" in scripts directory in DROMPA)
  • (hg18, hg19, mm9)
• Gene density Data (per 500k bp)
  • (hg19, mm10)
• Mappability Data
  • hg19 (28bp, 36bp, 50bp)
  • mm9 (28bp, 36bp, 50bp)
  • S. cerevisiae
• S. cerevisiae
  • Genome features (20140104) ("SGD_features.tab" obtained from Saccharomyces Genome Database)
  • Replication origin data (obtained from OriDB)
• S. pombe
  • Gene annotation data (gtf file obtained from Ensembl website)
  • Replication origin data (obtained from OriDB)