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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.
module load bwa/0.7.9a
export MM10=/cluster/tufts/genomes/MusMusculus/mm10/Sequence/BWAIndex/genome.fa
export MYDATADIR=/cluster/shared/myutln/mmdatabwa mem $MM10/genome.fa $MYDATADIR/myreads.fq >$MYDATADIR/myreads.sam
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Similarly, environmental variables can be set up, and in the case of bowtie2 BOWTIE2_INDEXES 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 ).
module load bowtie2
export BOWTIE2_INDEXES=/cluster/tufts/genomes/MusMusculus/mm10/Sequence/Bowtie2Index export MYDATADIR=/cluster/shared/myutln/mmdata bowtie2 -q -x genome -1 $MYDATADIR/myreads_1.fq -2 $MYDATADIR/myreads_2.fq -S myreads.sam