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06-07-2012, 08:18 AM
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Member
Location: France Join Date: Sep 2011
Posts: 52
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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 : Code:
bowtie2 -N 1 -L 18 --local Any ideas ? is this kind of mapping possible ? Thanks in advance for your reply. |
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