1. SACGF
  2. Untitled Project
  3. Attema_2013_200_enhancer

Overview

HTTPS SSH

Identification of an enhancer that increases miR-200b~200a~429 gene expression in breast cancer cells

Bash and Python scripts to produce data / graphs used in the paper:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075517

REQUIRED SOFTWARE

INSTALLATION

git clone https://bitbucket.org/sacgf/attema_2013_200_enhancer.git
cd attema_2013_200_enhancer
# Install python libraries
sudo pip install -r requirements.txt

Then edit the file scripts/config.sh, and set the variable:

TMAP_REFERENCE=

To the path to the genome.fa file in the TMAP index directory

RUNNING

./scripts/attema_2013_200_enhancer.sh
  • Separates fastq reads by RACE primers
  • Maps to HG19 with TMAP
  • Generates graphs, stats, bedgraph coverage files