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myillu_02_jellyfish.sh

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myillu_02_jellyfish.sh [2016/05/07 13:02]
hyjeong created
myillu_02_jellyfish.sh [2016/05/07 13:03] (current)
hyjeong
Line 2: Line 2:
  
   #!/bin/sh   #!/bin/sh
- +  ​
   export LD_LIBRARY_PATH=/​usr/​local/​apps/​jellyfish-2.2.3/​lib   export LD_LIBRARY_PATH=/​usr/​local/​apps/​jellyfish-2.2.3/​lib
   KMER=21   KMER=21
   THREADS=20   THREADS=20
- +  ​
   BASE=${1%%.*}   BASE=${1%%.*}
   echo "File name base: $BASE"   echo "File name base: $BASE"
- +  ​
   echo "​Running jellyfish..."​   echo "​Running jellyfish..."​
   jellyfish count -s 1G -m ${KMER} -t ${THREADS} -o kmer -C $1   jellyfish count -s 1G -m ${KMER} -t ${THREADS} -o kmer -C $1
   jellyfish dump -c -t kmer > ${BASE}.kmer${KMER}.txt   jellyfish dump -c -t kmer > ${BASE}.kmer${KMER}.txt
- +  ​
   echo "​Preparing histogram..."​   echo "​Preparing histogram..."​
   awk '​{print $2}' ${BASE}.kmer${KMER}.txt | sort -n | uniq -c | awk '​{print $2 ","​ $1}' > ${BASE}.jf.hist   awk '​{print $2}' ${BASE}.kmer${KMER}.txt | sort -n | uniq -c | awk '​{print $2 ","​ $1}' > ${BASE}.jf.hist
  
  
myillu_02_jellyfish.sh.txt ยท Last modified: 2016/05/07 13:03 by hyjeong