Publication Submitted:
Song Li, Louisa Liberman, Neelanjan Mukherjee, Philip N. Benfey, Uwe Ohler. (2013). Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Research.

About this study:
Pairs of RNA molecules transcribed from partially or entirely complementary loci are called cis-natural antisense transcripts (cis-NATs), and they play key roles in the regulation of gene expression in many organisms. A promising experimental tool for profiling sense and antisense transcription is strand-specific RNA sequencing (ssRNA-seq). To identify cis-NATs using ssRNA-seq, we developed a new computational method based on model comparison that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole root and cell-type specific Arabidopsis libraries confirmed most of the known cis-NAT pairs and identified hundreds of additional cis-NAT pairs.

• Download and install the required R, ROCR and DESeq package.
• Download the source code for NASTIseq from the link above.
• Linux:
  In the directory where you downloaded the source code, simply type "R CMD INSTALL NASTIseq_1.0.tar.gz".
  
  Or within an active R session, type:
  > install.packages('NASTIseq_1.0.tar.gz',repos=NULL,type='source')
  > library(NASTIseq)
  


• Windows:
  From the pull-down menu, click on "Packages->Install Packages from local zip file", and then select the downloaded file NASTIseq_1.0.zip