Hello, haukex, Thank you so much for your response. I tried to use makeBigWig.pl to transfer thefile to bigwig and I can visualize it in UCSC browser. Following is the protocol. Thank you again for your great help! Yue Li

To make bigWig files easier to generate, HOMER includes a program crea
+tively named "makeBigWig.pl" that automates all of the steps below.

makeBigWig.pl <tag directory> <genome> [special options] [makeUCSC fil
+e options] -webDir /path-to-web-fold/ -url http://webserverURL/bigwig
+Fold/
i.e. makeBigWig.pl PU.1-ChIP-Seq/ mm9  -webDir /var/www/bigWigs/ -url 
+http://ChuckNorrisU.edu/bigWigs/
[download]