Some useful commands - 18liedan/genomics_memo GitHub Wiki

Last updated: January 11th, 2026

keyboard shortcuts

control＋A 行の先頭までカーソルを移動 control + E 行の最後までカーソルを移動 control + K カーソルより後ろの文字を削除 control + L 現在の行が一番上になるように画面をスクロール（画面のクリア） control + H 直前の1文字を削除（backspace と同じ） control + D カーソルの位置の文字を削除（何も入力されていない時に行うとログアウト） alt + → 単語の区切れ目までカーソルを移動 alt + ← 同上

frequently used commands, etc.

echo $UID shows UID in ssh server htop checks CPU/RAM/etc. usage free -h checks RAM usage summary lscpu shows CPU details |: "pipe". It is used to pipe one command into another. That is, it directs the output from the first command into the input for the second command. command1 & command2: execute command2 after execution of command1 has finished command1 && command2: execute command2 only if execution of command1 has finished successfully command1 || command2: execute command2 only if execution of command1 has finished unsuccessfully

tmux for avoiding crashing

#for example
ssh a002

#make new session
tmux new -s session250203

#ctrlb then d detaches from session but runs in background

#go back to session
tmux attach-session -t session250203

nohup usage

nohup bash -c 'command here' > output.log
#e.g. combined with for loop
nohup bash -c 'for accession in $(cut -f 2 PRJDB13385-info.tsv); do printf "\n  Working on: ${accession}\n\n"; fasterq-dump --split-files ${accession} -e 16 -p; done' > PRJDB13385_output.log

move files without third party GUI

scp -P 22 file.ext [email protected]:~/directory

permanent path export:

#for the main softwares
echo 'export PATH="/lustre10/home/liedan/bwa-mem2-2.2.1_x64-linux/:${PATH}"' >> ~/.bashrc
echo 'export PATH="/lustre10/home/liedan/gatk-4.6.1.0/:${PATH}"' >> ~/.bashrc
echo 'export PATH="/lustre10/home/liedan/admixture_linux-1.3.0/:${PATH}"' >> ~/.bashrc
echo 'export PATH="/lustre10/home/liedan/angsd/:${PATH}"' >> ~/.bashrc
echo 'export PATH="/lustre10/home/liedan/RepeatMasker/:${PATH}"' >> ~/.bashrc

#refresh session
source ~/.bashrc

splitting big fasta into smaller ones

awk 'BEGIN {n_seq=0;} /^>/ {if(n_seq%1000==0){file=sprintf("myseq%d.fa",n_seq);} print >> file; n_seq++; next;} { print >> file; }' < sequences.fa

changing fastq to fasta

on a linux: cat input.fastq | awk 'NR % 4 == 1 {print ">" $0 } NR % 4 == 2 {print $0}' > output.fasta

on a mac: awk '(NR - 1) % 4 < 2' test.fq | sed 's/@/>/' > test.fa

filezilla set ssh key file

  1. Select Edit › Settings… › Connection › SFTP
  2. Press the Add key file… button
  3. Press Command-Shift-G to bring up a path selection window and type ~/.ssh
  4. Select the id_rsa key file and click Open (this imports the key)
  5. Click OK to close the Settings dialog
  6. Open File › Site Manager…
  7. Select the site with which you want to use the key
  8. Choose Protocol SFTP and select Logon Type Normal.
  9. If the file has a password, enter in the Password field.
  10. Click Connect and you see your files.