2.
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| Bioinformatics services |
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Bioinformatics services
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a
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For shell access to command line tools:
> ssh -Y emboss.uit.tufts.edu
For access to the web interface wEmboss.
For access to emboss web documentation.
Emboss tutorial
If you have any questions about Emboss related usage, applications, or assistance with software, please contact tts-research@tufts.edu.
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. Timings for Genome Mapping
The newest update to SLURM has better handling of backfill, which means if you specify a expected time for your program to run it can be placed earlier as nodes open up. Using sbatch you can specify a limit on the total run-time with -t or --time d-h:m:s. Times can be specified as min, min:sec, hr:min:sec, day-hr, day-hr:min, and day-hr:min:sec. So -t 5 means five minutes -t 5:00:00 is five hours.
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| #Sequences | BWA mem | Bowtie2 | Samtools |
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| 7 M | 1' 29" | 1' 39" | 1' 52" |
| 15 M | 3' 8" | 2' 30" | 3' 57" |
| 30 M | 6' 36" | 4' 53" | 5' 38" |
| 60 M | 12' 32" | 10' 6" | 10' 18" |
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b. 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.
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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 $MYDATADIR/myreads.sam |
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c. 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.
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Application performance is not always well documented and it may be beneficial to you to do some benchmarking. By doing so you will be in a position to better utilize the cluster resources. For example here is a benchmark examination of blastp and other tools.
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d. Tufts Center for Neuroscience Research Genomics Core
The Tufts CNR Genomics Core supplies links to bioinformatics resources related to their operation. See Tufts CNR Genomics Core Resources for more information.
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A separate server is used to support these services in some cases. However some software may require installation on the linux research cluster. Check the Installed Software for Bioinformatic software available on the cluster. To make a special request for software installation, please follow the instructions as noted elsewhere on this page.Emboss services can be found here