Difference between revisions of "Diamond"

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(Created page with "This is very fast alternative to the blastx program. This page contains some details about the program == key points made== * Describes blastx as the "gold standard" * high...")
 
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* Describes blastx as the "gold standard"  
 
* Describes blastx as the "gold standard"  
 
* highest value placed on sensitivity
 
* highest value placed on sensitivity
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 +
= Running in gridengine=
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 +
Here's a workable script
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 +
#!/bin/bash
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#$ -cwd
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#$ -j y
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#$ -S /bin/bash
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#$ -V
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#$ -q single.q
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#$ -pe multi 16
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module load diamond
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diamond blastx -p $NSLOTS -b 5 -d N95 -q 4440037.3.dna.fa -a N95 -t temp -e 0.000001 -k 1 -f tab
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diamond view -a N95.daa -o N95.m8

Revision as of 10:34, 21 April 2016

This is very fast alternative to the blastx program. This page contains some details about the program

key points made

  • Describes blastx as the "gold standard"
  • highest value placed on sensitivity

Running in gridengine

Here's a workable script

#!/bin/bash 
#$ -cwd 
#$ -j y
#$ -S /bin/bash 
#$ -V
#$ -q single.q
#$ -pe multi 16
module load diamond
diamond blastx -p $NSLOTS -b 5 -d N95 -q 4440037.3.dna.fa -a N95 -t temp -e 0.000001 -k 1 -f tab 
diamond view -a N95.daa -o N95.m8