Difference between revisions of "Tophat/Batch"

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(Created page with "You can submit a tophat job in batch mode with the following command: bsub [LSF options] "tophat [tophat options] <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,......")
 
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  bsub [LSF options] "tophat [tophat options] <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]"
 
  bsub [LSF options] "tophat [tophat options] <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]"
  
Here you need to replace ''[tophat options]'' with tophat command line options (please run <tt>tophat -h</tt> for getting a list of all command line options) and ''[LSF options]'' with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of <tt>bsub</tt>  on the wiki page about the [[Using_the_batch_system|batch system]].
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Here you need to replace ''[tophat options]'' with tophat command line options (please run <tt>tophat -h</tt> for getting a list of all command line options) and ''[LSF options]'' with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of <tt>bsub</tt>  on the wiki page about the [[Using_the_batch_system|batch system]]. Please have a look at https://ccb.jhu.edu/software/tophat/manual.shtml for more information about the input files (''<genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]'') that are required for running tophat.
 
 
Please have a look at https://ccb.jhu.edu/software/tophat/manual.shtml for more information about the input files (''<genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]'') that are required for running tophat.
 

Revision as of 14:25, 28 November 2016

You can submit a tophat job in batch mode with the following command:

bsub [LSF options] "tophat [tophat options] <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]"

Here you need to replace [tophat options] with tophat command line options (please run tophat -h for getting a list of all command line options) and [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system. Please have a look at https://ccb.jhu.edu/software/tophat/manual.shtml for more information about the input files (<genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]) that are required for running tophat.