--- a/README.md	Wed Sep 04 07:33:42 2019 -0400
+++ b/README.md	Thu Sep 05 09:04:56 2019 -0400
@@ -48,6 +48,55 @@
 if you want to do comparative analysis with RepeatExplorer and need to
 append sample codes to sequence identifiers
 
+### ChIP-Seq-mapper ###
+
+
+Analysis of NGS sequences from Chromatin Imunoprecipitation. ChiP and Input reads are mapped to contigs obtained from graph based repetitive sequence clustering to enriched repeats. This method was used in (Neumann et al. 2012). for identification of repetitive sequences associated with cetromeric region.
+
+#### Authors ####
+Petr Novak, Jiri Macas, Pavel Neumann, Georg Hermanutz
+
+Biology Centre CAS, Czech Republic
+
+
+#### Installation and dependencies ####
+
+ChIP-Seq-mapper require NCBI blast to be installed, R programming language with installed R2HTML and base64 packages and python3
+
+#### Usage ####
+
+```
+ChipSeqRatioAnalysis.py [-h] [-m MAX_CL] [-n NPROC] -c CHIPSEQ -i
+                               INPUTSEQ [-o OUTPUT] [-ht HTML] [-t THRESHOLD]
+                               -k CONTIGS
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -m MAX_CL, --max_cl MAX_CL
+                        Sets the maximum cluster number. Default = 200
+  -n NPROC, --nproc NPROC
+                        Sets the number of cpus to be used. Default = all
+                        available
+  -c CHIPSEQ, --ChipSeq CHIPSEQ
+                        Fasta file containing the Chip Sequences
+  -i INPUTSEQ, --InputSeq INPUTSEQ
+                        Fasta file containing the Input Sequences
+  -o OUTPUT, --output OUTPUT
+                        Specify a name for the CSV file to which the output
+                        will be save to. Default: ChipSeqRatio.csv                      
+  -ht HTML, --html HTML                                                                 
+                        Specify a name for the html report. Default :                   
+                        ChipSeqRatioReport                                              
+  -t THRESHOLD, --threshold THRESHOLD                                                   
+                        Optional plot filter. Default: mean ration between              
+                        Input hits and Chip hits.                                       
+  -k CONTIGS, --Contigs CONTIGS                                                         
+                        Contig file for blast 
+```
+
+####  References ####
+[PLoS Genet. Epub 2012 Jun 21. Stretching the rules: monocentric chromosomes with multiple centromere domains. Neumann P, Navrátilová A, Schroeder-Reiter E, Koblížková A, Steinbauerová V, Chocholová E, Novák P, Wanner G, Macas J.](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777)
+
 
 ## Dependencies ##