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Old 12-30-2010, 07:57 PM   #1
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Location: india

Join Date: Jul 2010
Posts: 1
Default Mapping Short Reads with unequal length using MAQ

hi everyone,

I m in the process of finding SNPs in miRNA sequence for which i have used known miRNA sequences as the reference and short reads of RNA sequence are mapped to it using MAQ.
The reads i m using is trimmed sequence so i dont supply the adapter sequence in the alignment option for MAQ.
The problem i m facing is in the alignment generated most of the reads are trimmed off automatically from the 3' end reducing it to 17 bp reads(original varies from 20,24,25). Some reads maintained thier original lenght in the alignment. And there is no obvious rule as to how the reads are trimmed(the trimmed length is not equal,).
Can anyone help me out?

Thanks in advance.
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