Data and Compute Setup

Course data downloads

Note

Some of these files are quite large. If you have issues downloading them, contact us at .

Compute setup

AWS Module

Connecting and properly using a cloud computing cluster at the CBW here

AMI

We have made our AWS AMI (Amazon Machine Image) publicly available. To launch your own instance, follow the instructions provided by Amazon on how to launch an EC2 instance from a custom Amazon Machine Image. Please note that you will need an AWS account to proceed, and that you will need to upload the CourseData files yourself.

Here are the details of the AMI:

  • AWS Region: us-east-1 (N. Virgina)
  • AMI type: public image
  • AMI name: CBW_EPI_231005
  • AMI ID: ami-0ae28d3f8e57ba8cf

If you want to create and activate a new AWS account, please follow the instructions provided by Amazon.

Software
conda

Install Miniconda by following the instructoion at Miniconda official site

bedtools
wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
mv bedtools.static.binary bedtools
chmod +x bedtools
bwa
wget https://newcontinuum.dl.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2
tar -jxvf bwa-0.7.17.tar.bz2
cd bwa-0.7.17/
make
#### FastQC
wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip
unzip fastqc_v0.12.1.zip
samtools
wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2
tar -jxvf samtools-1.17.tar.bz2
cd samtools-1.17
make
sudo make install
picard
wget https://github.com/broadinstitute/picard/releases/download/3.1.0/picard.jar
deeptools
pip install deeptools
MACS2
pip install MACS2
Homer
wget http://homer.ucsd.edu/homer/configureHomer.pl
perl ./configureHomer.pl -install
perl ./configureHomer.pl -install hg19
perl ./configureHomer.pl -install hg38
UCSC tools’
rsync -aP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/ ./
Biamark
wget https://github.com/FelixKrueger/Bismark/archive/refs/tags/v0.24.2.tar.gz
tar -zxf v0.24.2.tar.gz