{"id":4074,"date":"2019-09-30T11:51:39","date_gmt":"2019-09-30T10:51:39","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4074"},"modified":"2019-09-30T14:16:48","modified_gmt":"2019-09-30T13:16:48","slug":"star","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/star\/","title":{"rendered":"STAR"},"content":{"rendered":"

Overview<\/h2>\n

STAR<\/a> is a program to perform Spliced Transcripts Alignment to a Reference<\/p>\n

Versions 2.4.2a, 2.5.1a, 2.5.3a and 2.7.2b are installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing the software on the CSF. It is released under the MIT License<\/a> and all usage must adhere to that license.<\/p>\n

Set up procedure<\/h2>\n

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n

Load one of the following modulefiles:<\/p>\n

\r\n# Please note the different modulefile paths between versions!\r\n\r\n# Load one<\/strong> of the following modulefiles\r\nmodule load apps\/binapps\/star\/2.7.2b             # Also provides STARlong for long reads\r\n\r\nmodule load apps\/intel-18.0\/star\/2.7.2b          # Intel compiler version (might be faster\r\n                                                 # than the binapps<\/em> pre-compiled version)\r\n                                                 # Also provides STARlong for long reads\r\n\r\nmodule load apps\/star\/2.5.3a                     # ONLY provides STAR\r\n\r\n# These older versions and 'long reads' versions require you to first load:\r\nmodule load apps\/bioinf\r\n\r\n# Then you can load one of:\r\nmodule load apps\/star\/2.5.1a           # ONLY provides STAR\r\nmodule load apps\/star\/2.4.2a           # ONLY provides STAR\r\n\r\nmodule load apps\/star_long\/2.5.3a      # ONLY provides STARlong\r\nmodule load apps\/star_long\/2.4.2a      # ONLY provides STARlong\r\n\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run STAR on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
Serial batch job submission<\/h3>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\n# Load the modulefile for the version you require\r\nmodule load apps\/binapps\/star\/2.7.2b\r\n\r\n# $NSLOTS will be set to the number of cores requested (or 1 for a serial job)\r\nSTAR --runThreadN $NSLOTS --genomeDir REFERENCE<\/em> --readFilesIn R1.fq R2.fq<\/em>\r\n  #\r\n  # Use STARlong for 'long reads' version\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -pe smp.pe 8     # Number of cores (can be 2--32)\r\n\r\n# Load the modulefile for the version you require\r\nmodule load apps\/binapps\/star\/2.7.2b\r\n\r\n# $NSLOTS will be set to the number of cores requested (or 1 for a serial job)\r\nSTAR --runThreadN $NSLOTS --genomeDir REFERENCE<\/em> --readFilesIn R1.fq R2.fq<\/em>\r\n  #\r\n  # Use STARlong for 'long reads' version\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n