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jellyfish [2017/11/07 21:27]
jokinsey created
jellyfish [2017/11/07 21:40] (current)
jokinsey Added documentation for jellyfish
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 JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. If was developed by Guillaume Marçais and Carl Kingsford. You can find more information on JellyFish [[http://​www.cbcb.umd.edu/​software/​jellyfish/​|here]]. JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. If was developed by Guillaume Marçais and Carl Kingsford. You can find more information on JellyFish [[http://​www.cbcb.umd.edu/​software/​jellyfish/​|here]].
 +
 +====Enivironment Setup====
 +
 +To work with jellyfish first we need to load the module. The easiest way to do this is to modify the ''​.bashrc''​ file in your ''​$HOME''​ directory.
 +
 +<​code>​
 +module load jellyfish
 +</​code>​
 +
 +Then in your ''​$HOME''​ directory create another directory to submit your jellyfish jobs, and copy the ''​fasta''​ data file we will be using for the test job into the new directory.
 +
 +<​code>​
 +razor-l3:​jokinsey:​~$ mkdir JELLYFISH-JOBS
 +razor-l3:​jokinsey:​~$ cp /​share/​apps/​jellyfish/​jellyfish-1.1.10/​tests/​seq10m.fa JELLYFISH-JOBS/​
 +</​code>​
 +
 +====Example Job====
 +
 +To run the example job create a ''​PBS''​ script in the directory where you will submit the job and that has the necessary ''​fasta''​ file. The script will look like the one below.
 +
 +<​code>​
 +#!/bin/bash
 +#PBS -N jellyfish
 +#PBS -q tiny12core
 +#PBS -j oe
 +#PBS -o jellyfish.$PBS_JOBID
 +#PBS -l nodes=1:​ppn=12
 +#PBS -l walltime=1:​00:​00
 +
 +cd $PBS_O_WORKDIR
 +cp seq10m.fa ​ /​scratch/​$PBS_JOBID
 +cd /​scratch/​$PBS_JOBID
 +
 +jellyfish count -m 10 -o output -c 3 -s 10000000 -t 12 seq10m.fa
 +cp output $PBS_O_WORKDIR
 +</​code>​
 +
 +This will give us an ''​output''​ hash file that we can process with jellyfish. For more information on the flags we used see the manual [[http://​www.cbcb.umd.edu/​software/​jellyfish/​jellyfish-manual-1.1.pdf|here]].
 +
 +All thats left is to submit the job.
 +
 +<​code>​
 +razor-l3:​jokinsey:​~/​JELLYFISH-JOBS$ qsub jellyfish.pbs ​
 +</​code>​
 +
 +Once we have the ''​output''​ hash we can run other jellyfish operations with is like the ''​histo''​ operation shown below, which might be a way to verify your ''​output''​.
 +
 +<​code>​
 +razor-l3:​jokinsey:​~/​JELLYFISH-JOBS$ jellyfish histo output
 +1 742
 +2 3399
 +3 10929
 +4 26162
 +5 49704
 +6 78834
 +7 107855
 +8 128207
 +9 136220
 +10 129521
 +11 113132
 +12 89579
 +13 65480
 +14 44554
 +15 28390
 +16 16847
 +17 9360
 +18 4951
 +19 2493
 +20 1173
 +21 529
 +22 264
 +23 104
 +24 47
 +25 15
 +26 7
 +28 1
 +</​code>​
 +
 +
 +
jellyfish.txt · Last modified: 2017/11/07 21:40 by jokinsey