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al2na/sample.gse.sh

Last active August 29, 2015 14:08
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sample.gse.sh
#!/bin/bash
#$ -N run_bowtie
#$ -cwd
#$ -pe smp 2
#$ -l h_vmem=6G
infile=/data/bioinfo/genome_data/sample.ce10.fastq
outfile=~/my.alignment.sam
btindex=/data/bioinfo/genome_data/Caenorhabditis_elegans/UCSC/ce10/Sequence/BowtieIndex/genome
bowtie --chunkmbs 300 --best -m 1 -p 2 --phred33 -q $btindex $infile -S $outfile
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