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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