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Old 06-07-2012, 08:18 AM   #1
Location: France

Join Date: Sep 2011
Posts: 52
Default local mode alignement of reads

Dear all,
I'm trying to align reads in a local mode in order to obtain the same mapping as in attached file.
I want a seed of 18 nt allowing 1 mismatches but the mapping doesn't necessarily occur in the first bases of my reads; so i try this command line in bowtie2 :

bowtie2 -N 1 -L 18 --local
but it doesn't work
Any ideas ? is this kind of mapping possible ?
Thanks in advance for your reply.
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