Using RepeatMasker on Big Red

RepeatMasker is a program for finding and removing repeated low-complexity regions in DNA sequences. The current version on Big Red at Indiana University is 3.2.6. It is configured to use the REBASE database and cross-match search engines. A list of frequently asked questions about RepeatMasker is available online.

On this page:

1. Request a Big Red account
2. Send an academic user license agreement
3. Set up SoftEnv and submit jobs

Request a Big Red account

Access to Big Red is provided to all IU faculty and graduate students, and faculty-sponsored undergraduates and staff. Instructional use is limited to courses that have been approved by the Director for Research Technologies. If you use Big Red, you need to know the Big Red usage policies.

To request a Big Red account, use the Account Management System (AMS); see At IU, if I already have some computing accounts, how do I get others? For more, see Getting started on Big Red.

Send an academic license agreement

RepeatMasker is a restricted-use package available only to CAP3 group users. If you are at IU and want to use RepeatMasker, read the academic user agreement and see the registration form. Then email BIOS noting your agreement to the license terms, asking to use the RepeatMasker package on Big Red, and providing the information requested on these two web pages. After UITS staff receive the license agreements, you will be added as a CAP3 group member and will receive an email confirmation.

Set up SoftEnv and submit jobs

1. To set up your SoftEnv, edit your .soft file to add the line +RepeatMasker and execute the resoft command.
   
   
2. The introduction document file is available at /N/soft/linux-sles9-ppc64/Repeatmasker/RepeatMasker/repeatmasker.help.
   
   
3. To see the options for RepeatMasker, enter RepeatMasker or see /N/soft/linux-sles9-ppc64/Repeatmasker/RepeatMasker/RepeatMasker.
   
   
4. If your job will run for fewer than 20 minutes, call RepeatMasker in the directory where your input files are.

   If your program will run for longer than 20 minutes, use the serialjob command. For help, use the man command or see On Big Red at IU, how do I use the serialjob script to submit jobs?

Output that RepeatMasker generates will be in the same directory as your input files.

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