diffReps has two easy-to-use tools. One is for quick genomic annotation of a differential site or peak list. Another is for finding chromatin modification hotspots

1. Downoad

https://github.com/shenlab-sinai/diffreps/blob/master/README.md

1.1

git clone https://github.com/shenlab-sinai/diffreps.git

2. usage

diffReps.pl -tr C1.bed C2.bed C3.bed -co S1.bed S2.bed S3.bed -gn mm9 \
-re diff.nb.txt -me nb

diffReps requires input of BED files for ChIP-seq alignments for both treatment and control groups. BED files can be converted from any alignment format, such as BAM (Tip: you can use BedTools for this).

2.1 CHROMOSOME LENGTHS

It is important to supply diffReps with chromosome length information. diffReps requires that to bin the chromosomes into smaller sections. diffReps has a few genomes built-in so what you need to do is just give a genome name, such as mm9 or hg19. If the genome you are interested in is not already defined, you can give a text file for chorosome lengths. An example input is like

chr1 197195431
chr2 181748086
chr3 159599782
...

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