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Please read the documentation for a mapping program to understand the way in which the reference indexes are referred.
Examples
The examples listed below should be included in a script and then submitted
Example: BWA
It helps to set up environmental variables to avoid having to type long paths. Here a set of short reads ( myreads.fq) are mapped to the mouse genome (mm10) with a SAM formatted file as output. Note that bwa uses genome.fa as a reference index name and the bwa mem analysis is used. See the BWA documentation for other ways to invoke bwa.
module load bwa/0.7.9a export MM10=/cluster/tufts/genomes/MusMusculus/mm10/Sequence/BWAIndex export MYDATADIR=/cluster/shared/myutln/mmdata
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Similarly, environmental variables can be set up, and in the case of bowtie2 a BOWTIE2_INDEXES variable must be set also. Here we have an example of a paired end analysis, with minimal options. Note Bowtie2 uses genome as reference index name (-x genome ).
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d. HPC Modules for Bioinformatics
Note: some bioinformatic software modules, such as R modules like bioconductor or python modules, are not listed here because they are part of a larger module, for example R/3.1.0 or python/2.7.6. Load those modules to get to bioconductor or python modules such as numpy or matplotlib.
To list the entirety of the module collection use this command
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