An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

This tutorial includes an IPython notebook (Zika.ipynb) which contains a pipeline that describes the following steps: downloading data from SRA, analyzing RNA-Seq reads from SRA files to produce gene level read counts in analyze_sra.sh, normalizing read counts accomplished with normalize.R and perform data visualization, differential expression, and enrichment analyses.

The computational environment used in this tutorial is also 'Dockerized' and the resulting Docker image is available at: https://hub.docker.com/r/maayanlab/zika/.