Bartosz Kozak
bash Anaconda-latest-Linux-x86_64.sh
conda list
conda config --add channels r conda config --add channels conda-forge conda config --add channels bioconda
conda install -y sra-tools
fastq-dump -h
fastq-dump -X 5 -Z SRR390728
conda install -y fastqc
fastqc -h
conda install -y trimmomatic
java -jar ~/src/Trimmomatic-0.36/trimmomatic-0.36.jar
conda install -y cutadapt
cutadapt -h
conda install -y bioawk
bioawk
conda install -y samtools
samtools
conda install -y seqtk
seqtklub
seqtk seq
conda install -y bwa
bwa
_ Opis http://bowtie-bio.sourceforge.net/bowtie2/index.shtml (zalecam używanie wersji bowite2)
mkdir ~/scr/ cd ~/srclub (Ubuntu i dystrubucje oparte na Ubuntu)
curl -OL http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-linux-x8 6_64.zip unzip bowtie2-2.2.9-linux-x86_64.zip export PATH=~/src/bowtie2-2.2.9:$PATH
sudo apt-get install bowtie2
bowtie2
conda create -n tophat python=2 cd ~/src curl -kO https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.Linux_x86_64.tar.gz tar xzvf tophat-2.1.0.Linux_x86_64.tar.gz export PATH=~/src/tophat-2.1.0.Linux_x86_64:$PATH # wyświetla programy wchodzące w skład pakietu tophat ls ~/src/tophat-2.1.0.Linux_x86_64
tophat -h
conda install -y cufflinks
conda install -y hisat2
hisat2
conda install -y subread
featureCounts