diff --git a/KKsorghumEdgeR_v2.R b/EdgeR_analysis.R
similarity index 100%
rename from KKsorghumEdgeR_v2.R
rename to EdgeR_analysis.R
diff --git a/README.rst b/README.rst
index 7737bdc..05fd3ed 100644
--- a/README.rst
+++ b/README.rst
@@ -13,6 +13,9 @@ Contains a general pipeline for running RNASeq analysis. This involves convertin
Pipelines were developed in the `Brady Lab `_ at UC Davis
+RNAseq analysis outline provided by Oshlack et al. Genome Biology 2010 11:220 doi:10.1186/gb-2010-11-12-220
+
+
.. image:: http://genomebiology.com/content/figures/gb-2010-11-12-220-1-l.jpg
Oshlack et al. Genome Biology 2010 11:220 doi:10.1186/gb-2010-11-12-220
@@ -25,7 +28,8 @@ Installation
**Required Dependencies**
- - Instances are available on iplant "RNASeq analysis"
+ - Dependencies were installed onto iplant AMI "RNASeq Analysis v1"and are available through `atmosphere `_
+ - Requires bowtie, tophat, samtools, pysam, htseq, edgeR, python2.7
- Read `INSTALL file for instructions`
Obtaining an Alignment file
diff --git a/map_reads b/obtain_alignment.sh
similarity index 100%
rename from map_reads
rename to obtain_alignment.sh