From 1b30b2210a2917be57d3657a3a20124ace28fae3 Mon Sep 17 00:00:00 2001 From: Gina Turco Date: Tue, 30 Apr 2013 17:27:57 -0700 Subject: [PATCH] cleaned up readme and renamed files --- KKsorghumEdgeR_v2.R => EdgeR_analysis.R | 0 README.rst | 6 +++++- map_reads => obtain_alignment.sh | 0 3 files changed, 5 insertions(+), 1 deletion(-) rename KKsorghumEdgeR_v2.R => EdgeR_analysis.R (100%) rename map_reads => obtain_alignment.sh (100%) 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