install latest Cufflinks

See here.

install latest TopHat

See here.

sort GTF

(grep "^#" file.gtf; grep -v "^#" file.gtf | sort -k1,1 -k4,4n) > file_sorted.gtf
will first write all comments (lines beginning with #) tofile_sorted.gtf, then all other lines sorted first by the first column, alphanumerically, second by the fourth column, numerically. This works as well for files that do not contain comments. Sort compressed:
(zgrep "^#" file.gtf; zgrep -v "^#" file.gtf | sort -k1,1 -k4,4n) | gzip > file_sorted.gtf.gz

tree as an alternative to ls

ls -lha
total 1,2G
drwxrwxr-x 3 alex alex 4,0K Nov 15 09:48 .
drwxr-xr-x 4 alex alex 4,0K Nov 14 15:46 ..
drwxrwxr-x 4 alex alex 4,0K Nov 15 09:41 Homo_sapiens
-rw-rw-r-- 1 alex alex 1,2G Nov 15 10:17 Homo_sapiens_Ensembl_GRCh37.tar.gz
tree -pfuih --du
.
[drwxrwxr-x alex     215G]  ./Homo_sapiens
[drwxrwxr-x alex      52G]  ./Homo_sapiens/Ensembl
[drwxrwxr-x alex      52G]  ./Homo_sapiens/Ensembl/GRCh37
[drwxrwxr-x alex      30G]  ./Homo_sapiens/Ensembl/GRCh37/Annotation
[drwxrwxr-x alex      30G]  ./Homo_sapiens/Ensembl/GRCh37/Annotation/Archives
[drwxrwxr-x alex     525M]  ./Homo_sapiens/Ensembl/GRCh37/Annotation/Archives/archive-2010-09-28-01-21-46
[-rwxrwxr-x alex      302]  ./Homo_sapiens/Ensembl/GRCh37/Annotation/Archives/archive-2010-09-28-01-21-46/ChromInfo.txt
[..]

wget: download in background, resume download

wget -bqc
  • -b Go to background immediately after startup. If no output file is specified via the -o, output is redirected to wget-log.
  • -q Turn off Wget’s output.
  • -c Continue getting a partially-downloaded file. This is useful when you want to finish up a download started by a previous instance of Wget, or by another program.
Monitor download speed using
sudo iotop

fix ssh file permissions

user@client~$ chown $USER:$USER -R $HOME/.ssh
user@client~$ chmod 700 $HOME/.ssh
user@client~$ find $HOME/.ssh/ -type f -exec chmod 600 {} +
user@client~$ find $HOME/.ssh/ -type f \( -name '*.pub' \) -exec chmod 644 {} +
Assuming that your public key files are named anything ending with “.pub”. Use the find command to recursively (see as well here) set file permissions. This allows you to organize multiple key files into subdirectories within the .ssh folder.

copy folders recursively via ssh (no password but key file)

From local to remote: From remote to local: