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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 --------------------
diffReps/1.55.1 
[user@biowulf]$
[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
[user@biowulf]$

diffReps.pl
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.

[user@biowulf]$
[user@biowulf]$ diffReps.pl
Usage: diffReps.pl --treatment bed_file1...[bed_fileN] --control bed_file1...[bed_fileN] --report output_results \
           [--gname genome_name|--chrlen chrom_length_file]
[user@biowulf]$ 

elandsorted2bed.pl
Convert ELAND sorted.txt to sorted bed.6.txt

[user@biowulf]$ elandsorted2bed.pl
Usage: ../../bin/elandsorted2bed.pl eland_sorted_file [phred_score_cutoff(Default=0)]
[user@biowulf]$

export2sorted.pl
Convert ELAND export.txt to sorted.txt

[user@biowulf]$ export2sorted.pl
Usage: ../../bin/export2sorted.pl in_export.txt out_sorted.txt
[user@biowulf]$

findHotspots.pl
Identify chromatin modification hotspots from differential analysis results.

[user@biowulf]$ findHotspots.pl
Usage: findHotspots.pl --diff diff_file1..[diff_fileN] --output output_file \
         [--pval p_value_cutoff] [--infocol info_cols_output]
[user@biowulf]$

refgene_getnearestgene

[user@biowulf]$
[user@biowulf]$ refgene_getnearestgene
Usage: refgene_getnearestgene     
 -d path of refgene database      
   *   *   *
[user@biowulf]$

region_analysis.pl
Analyze a set of regions by mapping them to various genomic features.

[user@biowulf]$
[user@biowulf]$ region_analysis.pl
Usage: ../../bin/region_analysis.pl --input in_reg_list [--rhead] [--help] [--database refseq(default)|ensembl] [--genome mm9(default)]
[user@biowulf]$

rmdup_sorted_bed.pl
Remove redundant reads from sorted BED file.

[user@biowulf]$
[user@biowulf]$ rmdup_sorted_bed.pl
Usage: ../../bin/rmdup_sorted_bed.pl in_sorted.bed out_nonredundant.bed dup_allowed
[user@biowulf]$

sam2bed.pl
Convert SAM format to BED6 format.

[user@biowulf]$
[user@biowulf]$ sam2bed.pl
Usage: ../../bin/sam2bed.pl input.sam output.bed [-u]
[user@biowulf]$

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

Documentation