adding a full example of the analysis of the Oxytricha trifallax organism

diff --git a/README b/README
index b77f87b..2f4a236 100644
--- a/README
+++ b/README
@@ -483,6 +483,32 @@ where the file "sample.input" contains the following files:
 	alnSRX483017_1.fastq.gz-sorted.bam


+IV.iv) Full analysis of Oxytricha trifallax
+	We describe the ste-by-step case of how to analyze the data for the Oxytricha trifallax
+
+	# 1) create a directory where allocate the data
+	mkdir oxy
+	cd oxy
+
+	# 2) use the auxiliary tools we provide to download the datasets for Oxytricha trifallax
+	# 2.i) first the reference genome
+	PATHtoRACSrepo/datasets/get....
+	# 2.ii) now the ChIP-seq data, you will the NCBI-SRA toolkit for this step!
+	PATHtoRACS/repo/datasets/get...
+
+	# 3) determination of ORFs with RACS
+	PATHtoRACSrepo/core/countReads.sh  SRX483016_1.fastq.gz  SRX483017_1.fastq.gz  Oxytricha_trifallax_022112_assembly.fasta  Oxytricha_trifallax_022112.gff3  /dev/shm/  16  PATHtoRACS/core/defns/OXY_gene.idf
+
+	# 4) determination of the IGRs
+	# 4.i) first, cd into the ORF_... directory generated by the previous step where the results from the ORF part of the RACS pipeline were placed
+	cd ORF_...
+	# 4.ii) create the "sample.input" file containing the bames of the *.fastq.gz files to be processed, eg.
+	ls -1 *fastq.gz-sorted.bam > sample.input
+	# 4.iii) run the IGR determination part of the RACS pipeline
+	PATHtoRACSrepo/core/intergenic/det-interGenes.sh FINAL.table.SRX483016_1-SRX483017_1 Oxytricha_trifallax_022112.gff3 interGENs_run1_OXY.csv  sample.input
+
+
+
 V) comparison to MACS and Other Tools
 	--- in prep. ---