I just found out that TreeView is great to have a general heatmap of our RNAseq samples (Transcriptome). I installed TreeView on my computer and had a look at there sample files, though their website isn't really helping and I don't know where to start.

http://jtreeview.sourceforge.net/

**Is there any good manual or tutorial to get started with TreeView**?
Its straight forward with usage and also it has nice [manual][1]. Once you get your expression data (generally log transformed and normalized) you cluster them using [cluster 3.0][2]. Cluster generates mainly 3 files.

1. .cdt (cluster data) file which is the one you open with TreeView. It contains the same expression table that you used for clustering except the data has be re organised according to clustering.
2. .gtr and .atr (gene tree and array tree) contain structure of your expression data and your arrays (in this case RNA-seq replicates and samples).
3. If you are using k-mean clustering you will have .kgg file.

Once you are done with clustering, you open .cdt file with TreeView. If the heatmap which shows up is not visible clearly, go to settings -> pixel settings and change contrast.

You can search for your gene in analysis tab with find genes. You can export the image as png or jpeg. You can also do PCA and other stuffs, you will have to play around.

Remember that cluster generally crashes with low memory computer when you have thousands of gene.

 [1]: http://jtreeview.sourceforge.net/docs/JTVUserManual/single.html
 [2]: http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm