Ghana-Installation-software.md

@@ -102,3 +102,30 @@ Add /usr/local/bowtie2-2.3.4.3 to the path :
 ### Usage:
 
            bowtie2 + arguments
+
+
+# tophat2:
+
+TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. 
+
+
+URL: https://ccb.jhu.edu/software/tophat/index.shtml
+
+
+### Installation:
+
+         wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz
+         tar xvfz tophat-2.1.1.tar.gz 
+         cd tophat-2.1.1
+         ./configure --prefix=/usr/local/tophat-2.1.1
+         make 
+         make install
+                 
+Add /usr/local/tophat-2.1.1 to the path :
+
+       echo  'export PATH=/usr/local/tophat-2.1.1:$PATH' >>/etc/profile
+       source /etc/profile
+
+### Usage:
+
+           tophat2 + arguments