Lab 7: Analyze transcriptome¶
BUSCO: http://busco.ezlab.org/ and http://bioinformatics.oxfordjournals.org/content/31/19/3210
> Step 1: Launch and AMI. For this exercise, we will use a c4.2xlarge instance. ADD A 100GB HARD DRIVE TO YOUR INSTANCE
ssh -i ~/Downloads/?????.pem ubuntu@ec2-???-???-???-???.compute-1.amazonaws.com
> Update Software
sudo apt-get update && sudo apt-get -y upgrade
> Install other software
sudo apt-get -y install hmmer cmake tmux git curl bowtie libncurses5-dev samtools gcc make ncbi-blast+ g++ python-dev libboost-iostreams-dev libboost-system-dev libboost-filesystem-dev
> Install busco
cd
curl -LO http://busco.ezlab.org/files/BUSCO_v1.1b1.tar.gz
tar -zxf BUSCO_v1.1b1.tar.gz
cd BUSCO_v1.1b1
PATH=$PATH:$(pwd)
curl -LO http://busco.ezlab.org/files/metazoa_buscos.tar.gz
tar -zxf metazoa_buscos.tar.gz
> install augustus
cd
curl -LO http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.0.2.tar.gz
tar -zxf augustus-3.0.2.tar.gz
cd augustus-3.0.2/
make
PATH=$PATH:$(pwd)/bin:$(pwd)/scripts
export AUGUSTUS_CONFIG_PATH=/home/ubuntu/augustus-3.0.2/config/
> Download assemblies from last week.
mkdir $HOME/assembly && cd $HOME/assembly
curl -LO https://s3.amazonaws.com/gen711/trim2.corr.trinity.Trinity.fasta
curl -LO https://s3.amazonaws.com/gen711/trim20.corr.trinity.Trinity.fasta
> Run BUSCO: do ONE of these.. coordinate with your neighbor so that s/he is doing the other.
mkdir $HOME/busco && cd $HOME/busco
ln -s $HOME/BUSCO_v1.1b1/metazoa .
#do this one
python3 ~/BUSCO_v1.1b1/BUSCO_v1.1b1.py -g ../assembly/trim20.corr.trinity.Trinity.fasta -m Trans --cpu 8 -o trim20 -l metazoa
#or this one
python3 ~/BUSCO_v1.1b1/BUSCO_v1.1b1.py -g ../assembly/trim2.corr.trinity.Trinity.fasta -m Trans --cpu 8 -o trim2 -l metazoa
> look at BUSCO results
#do whichever of these commands that pertain to the BUSCO run you chose to do above.
more run_trim20/short*
more run_trim2/short*
> What is a BUSCO anyway - see http://bioinformatics.oxfordjournals.org/content/31/19/3210. How do the assemblies differ?