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UNIX WIZARDRY

The explicit goal of this tutorial is to provide you with some tricks and tools and to make your unix life happier. Also, to possibly introduce you to samtools.


See https://github.com/stephenturner/oneliners for a bunch of examples.


LAUNCH AN INSTANCE: Get something small, for instance t2.small and update it.

sudo apt-get update && sudo apt-get -y upgrade
sudo apt-get -y install libncurses5-dev build-essential tmux git gcc make g++ python-dev unzip default-jre zlib1g-dev

ALIASES: These are 'shortcuts' for make doing stuff more efficient.

alias c='clear'
alias gh='history | grep'
alias ll='logout'
alias l='ls -lth'
alias mv='mv -i'
alias cp='cp -i'
alias targz='tar -zcf'
alias utargz='tar -zxf'

alias tn="tmux new -s"
alias ta="tmux attach -t"
alias tl="tmux ls"
alias tk="tmux kill-session -t"

INSTALL TRINITY: note the -j4

git clone https://github.com/trinityrnaseq/trinityrnaseq.git
cd trinityrnaseq
make -j4
PATH=$PATH:$(pwd)

.profile customization

nano ~/.profile

DOWNLOAD SOME DATA

mkdir /home/ubuntu/data
cd /home/ubuntu/data
curl -LO https://www.dropbox.com/s/5fymuyb1f2l8kfj/ngsfile.tar.gz
utargz ngsfile.tar.gz

Find a file

cd $HOME
find / -name Trinity.fasta
find / -type f -size +10M 2> /dev/null

sed

cd /home/ubuntu/data/ngs2015
less Trinity.fasta
sed 's_|_-_g' Trinity.fasta | grep ^'>' | head
sed -i 's_|_-_g' Trinity.fasta

Number fasta def line

awk '/^>/{print ">" ++i; next}{print}' < Trinity.fasta > Trinity.numbered.fasta

awk

less Trinity.counts.RNAseq.txt
awk '{print $1 "\t" $3}' Trinity.counts.RNAseq.txt | head
awk '$1 == "c996_g1_i1"' Trinity.counts.RNAseq.txt

Random Stuff

cd -
tmux/screen

SAMTOOLS

Let's learn something about samtools

INSTALL

cd $HOME
git clone https://github.com/samtools/htslib.git
cd htslib && make -j4 && cd ../
git clone https://github.com/samtools/samtools.git
cd samtools && make -j4 && PATH=$PATH:$(pwd) && cd ../

EXPLORE

cd $HOME/data/ngs2015

samtools sort ngs.bam -o test.sort.bam -O bam -T temp

samtools index test.sort.bam

samtools idxstats test.sort.bam | less

samtools bam2fq -s from.bam.se.fq --reference Trinity.fasta test.sort.bam > from.bam.pe.fastq

samtools depth -a test.sort.bam | grep 'TR1|c0_g1_i1' | less
samtools depth -a test.sort.bam | awk '$1 == "TR1|c0_g1_i1"' | less

samtools flagstat test.sort.bam

samtools view -h test.sort.bam > test.sort.sam

samtools view -hs 0.1 test.sort.bam > test.subsamp.sam

TERMINATE YOUR INSTANCE