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Old 06-10-2014, 07:30 AM   #14
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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The -x option is for bowtie2. You want
Code:
/home/carolw/Desktop/bowtie-1.0.1/bowtie -r -S /home/carolw/Desktop/bowtie-1.0.1/indexes/g1_bt1_index /home/carolw/rawSeq /home/carolw/rawSeq /home/carolw/rawSeq.sam
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