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  • #1

    bowite query about miRNA-seq

    Hello all,
    I have aligned miRNA short reads by bowtie with -n 1 -l 18 and was expected mapped output with not less than 18 nt as i have restricted with flag -l 18 (seed). But i really not satisfied with bowtie output as i got some reads with 17M and 16M mapped with genome. Could someone please explain this why its happened ???

    Thanks in advance
    Last edited by unique379; 12-10-2013, 04:16 AM.
    Tags: bioinfomatics, bowtie, mirna-seq, ncrna
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