Advanced Command-Line

1. Advanced Pipes

mkdir advanced
cd advanced
ls /home | cut -c1 | sort | uniq -c
ln -s /share/biocore-archive/Leveau_J_UCD/RNASeq_Arabidopsis_2016/00-RawData/C61_S67_L006/C61_S67_L006_R*_001.fastq.gz .
zcat C61_S67_L006_R1_001.fastq.gz | sed -n '1~4p' | cut -d: -f10 | sort | uniq -c

2. Process substitution

module load sickle scythe
wget https://ucdavis-bioinformatics-training.github.io/2017-June-RNA-Seq-Workshop/tuesday/adapters.fasta
zcat C61_S67_L006_R1_001.fastq.gz | head -400000 > r1.fq
sickle se -f <(scythe -a adapters.fasta r1.fq) -t sanger -o trimmed.fa

zcat C61_S67_L006_R2_001.fastq.gz | head -400000 > r2.fq
sickle pe -f <(scythe -a adapters.fasta r1.fq) -r <(scythe -a adapters.fasta r2.fq) -t sanger -o trimmed1.fa -p trimmed2.fa -s single.fa

3. The ‘sed’ command

cp /usr/share/common-licenses/BSD .
head BSD | sed 's/Redistribution/Mangling/'
sed '4q;d' BSD

sed tutorial

4. for loops

for x in /share/biocore-archive/Leveau_J_UCD/RNASeq_Arabidopsis_2016/00-RawData/*/*; do basename $x; done
for x in /share/biocore-archive/Leveau_J_UCD/RNASeq_Arabidopsis_2016/00-RawData/*/*; do NAME=`basename $x`; echo $NAME is a file; done

5. find

find /share/biocore/joshi/projects/genomes -name "*.fa"
find /share/biocore/joshi/projects/genomes -name "*.fa" -exec ls -l {} \;

6. xargs

find /share/biocore/joshi/projects/genomes -name "*.fa" | xargs ls -lh

7. Installing software and git

git clone https://github.com/najoshi/sickle.git
cd sickle
cat Makefile
make

Now you need to edit your PATH.

8. .bashrc/.bash_profile and aliases setup & the PATH variable

9. Intro to perl

10. Intro to mysql

wget https://ucdavis-bioinformatics-training.github.io/2017-June-RNA-Seq-Workshop/monday/db.sqlite3
sqlite3 db.sqlite3

11. Intro to python