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diffReps on Helix & Biowulf
Detecting differential chromatin modification sites from ChIP-seq data with biological replicates

ChIP-seq is now widely used to profile the enrichment of a DNA-binding protein on a genome. It is of high interest to compare the binding differences of a histone mark or transcription factor between two contrasting conditions, such as disease vs. control.

diffReps is developed to serve this purpose. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. diffReps takes into account the biological variations within a group of samples and uses that information to enhance the statistical power.

diffRefs is a collection of perl software.

diffReps Commands
To run command files, add the path "/usr/local/perl-5.12.1-threads" to your PATH environment variable. This is easily done by using the module command, as in the example:

[user@biowulf]$ module avail diffRep            (see what versions are available)

------------------- /usr/local/Modules/3.2.9/modulefiles --------------------
[user@biowulf]$ module load diffReps            (load the default version)
[user@biowulf]$ module list                     (see what version is loaded)
Currently Loaded Modulefiles:
  1) diffReps/1.55.1
Perform sliding window differential analysis to identify chromatin modification sites for ChIP-seq data from two groups of samples. Assume the two groups are treatment and control.

Usage: --treatment bed_file1...[bed_fileN] --control bed_file1...[bed_fileN] --report output_results \
           [--gname genome_name|--chrlen chrom_length_file]
Convert ELAND sorted.txt to sorted bed.6.txt

Usage: ../../bin/ eland_sorted_file [phred_score_cutoff(Default=0)]
Convert ELAND export.txt to sorted.txt

Usage: ../../bin/ in_export.txt out_sorted.txt
Identify chromatin modification hotspots from differential analysis results.

Usage: --diff diff_file1..[diff_fileN] --output output_file \
         [--pval p_value_cutoff] [--infocol info_cols_output]


[user@biowulf]$ refgene_getnearestgene
Usage: refgene_getnearestgene     
 -d path of refgene database      
   *   *   *
Analyze a set of regions by mapping them to various genomic features.

Usage: ../../bin/ --input in_reg_list [--rhead] [--help] [--database refseq(default)|ensembl] [--genome mm9(default)]
Remove redundant reads from sorted BED file.

Usage: ../../bin/ in_sorted.bed out_nonredundant.bed dup_allowed
Convert SAM format to BED6 format.

Usage: ../../bin/ input.sam output.bed [-u]

diffReps Packages
diffReps Databases
  • hg19.RefSeq.refFlat.cisgenome.txt
  • hg19.ensembl.refFlat.cisgenome.txt
  • hg19.genedeserts.bed
  • hg19.pericentromeres.bed
  • hg19.subtelomeres.bed
  • mm9.RefSeq.refFlat.cisgenome.txt
  • mm9.genedeserts.bed
  • mm9.ensembl.refFlat.cisgenome.txt
  • mm9.pericentromeres.bed
  • mm9.subtelomeres.bed
  • rn4.RefSeq.refFlat.cisgenome.txt
  • rn4.genedeserts.bed
  • rn4.ensembl.refFlat.cisgenome.txt
  • rn4.pericentromeres.bed
  • rn4.subtelomeres.bed