Generate Random Genomic Positions

Generating random genomic positions or coordinates can be useful in comparing characteristics of a set of genomic loci to that what would be expected from permutations of the underlying genomic distribution.  Below is a Python script to aid in selecting random genomic positions.  The script chooses a chromosome based on probabilities assigned by chromosome length and then chooses a chromosomal position from a uniform distribution of the chromosome's length.  An added gap checking statement is included to ensure the chosen position lies within the accessible genome.  You can choose the number of positions you want, the number of permutations to conduct, the size of the genomic positions, and the genomic build of interest.  A UNIX shell script is included as a wrapper to automatically download needed chromosomal gap and cytoband files as well as run the Python script.  Useage for the UNIX script can be seen by typing ./make_random.sh from the command line after giving the script executable privileges.  An example command would be ./make_random 100 10 1000 hg19.  This command would make 10 .bed files each with 100 random 1Kb genomic regions from the hg19 genome build.  Below are the make_random.sh and make_random.py scripts.

Generate Public/Private RSA Key Pair for SFTP

To access an SFTP server, an SSH public key must be created and shared with the SFTP host.  To generate a public/private key pair the ssh-keygen utility in UNIX can be used.  This program will calculate a key pair for you by following these steps:

(1) At the UNIX prompt, type ssh-keygen.  A message will appear indicating the application is generating the public/private rsa key pair.

(2) You will next be prompted to enter the location where you want to save the key.  You can specify a filename or just leave the space blank and press Enter.

(3) Afterwards you will be prompted to enter a passphrase to use as a password.  Enter your passphrase here or you can opt to leave the space blank.  It is acceptable to simply hit Enter to proceed without specifying a passphrase.

(4) Finally, you will be prompted to re-enter your passphrase.

That is all there is to creating a public and private key pair.  To access the remote SFTP server the administrator will need you to forward a copy of your public key to set up your account.  The public key will be a file with one line that includes "ssh-rsa", a long key code, followed by your account name and host name (ex: user@host.school.edu).  The file extension will be .pub.