--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq/README.md	Wed Jan 09 18:39:12 2013 -0500
@@ -0,0 +1,23 @@
+# sam2counts and DESeq in Galaxy
+
+## About
+
+This is a Galaxy package that wraps sam2counts and DESeq for RNA-Seq analysis using a transcriptome reference.  sam2counts takes SAM or BAM files that are created from an alignment to a transcriptome and creates counts of aligned reads for each transcript.  DESeq uses the DESeq package from Bioconductor in R and analyzes the count data from sam2counts. DESeq outputs a toptable of transcripts sorted by adjusted p-value and a page of diagnostic plots.
+
+## Requirements
+
+Python 2.6.5
+pysam 0.6 (package for Python)
+R 2.15
+Bioconductor 2.10 (package for R)
+DESeq 1.8.3 (package for R)
+aroma.light 1.24.0 (package for R)
+lattice 0.20-6 (package for R)
+
+## Installation
+
+stderr_wrapper.py and sam2counts_galaxy.py must be in the path or they can remain in the tools directory with the xml files.  deseq.R must be copied to the "tool-data" directory under the main Galaxy install directory.
+
+## Use
+
+sam2counts needs a SAM file (produced by aligning to a transcriptome) with header information as the input.  The count data produced from this SAM file gets fed into DESeq.