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c. Genome Indexes on Cluster
Several mammalian and model system genomes, indexes, and annotations are located on the Tufts HPC cluster. Currently the genomes are listed below in the indicated directory tree are UCSC genome builds, except for canFam3 which is a NCBI build.
/cluster/tufts/genomes
/HomoSapiens
/hg18
/hg19
/MusMusculus
/mm9
/mm10
/RattusNorvegicus
/rn4
/rn5
/CanisFamiliaris
/canFam2
/canFam3
/DrosophilaMelanogaster
/canFam2
dm3
/CaenorhabditisElegans
/canFam3ce10 Within each build subdirectory, there are two subdirectories.
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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 $MYDATADIR/myreads.sam
d. HPC Modules for Bioinformatics
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