diff --git a/README.md b/README.md
index 378a84f..e457067 100644
--- a/README.md
+++ b/README.md
@@ -81,11 +81,15 @@ The genome aligner BWA (http://bio-bwa.sourceforge.net) is downloaded and compil
                  -map genome-hic.map -plot genome-hic-length.png -file 0 \
                  genome-scaffhic.fasta GM12878-HiC_1.fastq.gz GM12878-HiC_2.fastq.gz genome-hic2.fasta \
           
-           You now have  \
-              1. Scaffolded assembly file genome-scaffhic.fasta; \
-              2. HiC map genome-hic.map; \ 
+           You now have  
+              1. Scaffolded assembly file genome-scaffhic.fasta; 
+              2. HiC map genome-hic.map;  
               3. HiC length distribution image genome-hic-length.png 
-
+              4. Assembly file produced in the visualization step:  genome-hic2.fasta 
+                 This file is not used, but it might be slightly better than genome-scaffhic.fasta 
+                 The visualization results are based on genome-scaffhic.fasta 
+                 
           To view it on a desktop linux or Mac laptop use PretextView https://github.com/wtsi-hpag/PretextView  \
-          $ ./PretextView genome-hic.map 
-        
+          $ ./PretextView genome-hic.map
+
+