hiCLIP reveals the atlas of mRNA secondary structures recognized by Staufen 1

This package performs analysis of high-throughput sequencing data produced by hiCLIP, mRNA-Seq and ribosome profiling.

1. Data analysis summary

a. High-throughput sequence data The fastq files are available from ArrayExpress with the following access codes: iCLIP and hiCLIP: E-MTAB-2937, mRNA-Seq: E-MTAB-2940, ribosome profiling: E-MTAB-2941.

b. Demultiplexing libraries Fastq files were demultiplexed.

c. Data pre-processing Data such as gtf and fasta files were downloaded and parsed for the analysis. Part c and e are implemented as Sweave scripts.

d. Mapping of high-throughput sequencing reads hiCLIP, ribosome profiling and mRNA-Seq data were mapped.

e. Analyzing high-throughput sequencing data. The analysis produces plots for the major figures used in the manuscript and performs the associated statistical analyses.

f. Data visulaization of hybrid reads with IGV The hybrid reads were visualized with IGV-2.1.20. The following files were visualized with IGV:


    Genome: data/processed/fasta/longest_mRNA_and_ncRNA.fa

    Transcript coordinate: data/processed/gtf/gr_tc_longest_gene_IGV.gtf

    IGV compatible sam files for hiCLIP data: results/manuscript/IGV/

g. Data visualization of hybrid reads with Circos plot The hybrid reads were visualized using Circos plot, and the scripts and the data for the visualization are located in the "R/visulalization_circos_plot folder"

2. ENVIRONMENT

Tested on Linux.

3. USAGE

python run_analysis.py -d /path/to/STAU1_hiCLIP -p /path/to/Python-2.7.1 -r /path/to/R-2.15.1

Below is the example code to run the analysis.


qsub -b y ~/Python-2.7.1/python /user/STAU1_hiCLIP/exec/run_analysis.py -d /user/STAU1_hiCLIP -p ~/Python-2.7.1 -r ~/R-2.15.1

4. PREREQUISITE

Python-2.7.1, R-2.15.1 and pdflatex have to be installed.
R packages described in the methods section should be installed in R-2.15.1/library/
All other binary packages described in the methods section have to be compiled and located under bin/ directory.

5. ACKNOWLEDGEMENT

The package was developed by Yoichiro Sugimoto with the help of Kathi Zarnak and Nejc Haberman by referring to Python Cookbook, R Graphics Cookbook and online discussions, and the scripts in R/visulalization_circos_plot folder were written by Elodie Darbo�. If any acknowledgement is missing, please let us know.

ulelab / STAU1_hiCLIP