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2019년 11월 교육 자료

myillu_02_jellyfish.sh

This is an old revision of the document!


Script <myIllu_02_jellyfish.sh>

#!/bin/sh

export LD_LIBRARY_PATH=/usr/local/apps/jellyfish-2.2.3/lib

KMER=21
THREADS=20

BASE=${1%%.*}

echo "File name base: $BASE"

echo “Running jellyfish…”

jellyfish count -s 1G -m ${KMER} -t ${THREADS} -o kmer -C $1
jellyfish dump -c -t kmer > ${BASE}.kmer${KMER}.txt

echo “Preparing histogram…”

awk '{print $2}' ${BASE}.kmer${KMER}.txt | sort -n | uniq -c | awk '{print $2 "," $1}' > ${BASE}.jf.hist
myillu_02_jellyfish.sh.1462593772.txt.gz · Last modified: 2016/05/07 13:02 by hyjeong