| layout | permalink | title | header1 | header2 | image | length |
|---|---|---|---|---|---|---|
workshop_main_3day |
/EPI_2023_tools |
Epigenomic Data Analysis |
Workshop Pages for Students |
Epigenomic Analysis 2023 |
/site_images/CBW_Epigenome-data_icon.jpg |
3 days |
Install Miniconda by following the instructoion at Miniconda official site
wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
mv bedtools.static.binary bedtools
chmod +x bedtools
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
wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip
unzip fastqc_v0.12.1.zip
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
wget https://github.com/broadinstitute/picard/releases/download/3.1.0/picard.jar
pip install deeptools
pip install MACS2
wget http://homer.ucsd.edu/homer/configureHomer.pl
perl ./configureHomer.pl -install
perl ./configureHomer.pl -install hg19
perl ./configureHomer.pl -install hg38
rsync -aP hgdownload.soe.ucsc.edu::genome/admin/exe/linux.x86_64/ ./
wget https://github.com/FelixKrueger/Bismark/archive/refs/tags/v0.24.2.tar.gz
tar -zxf v0.24.2.tar.gz