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  • mapping reads to known miRNAs precursors

    Dear all,
    I'm trying to estimate the all reads count that are mapped to a specific precursor. I have done it my using bowtie with no mistmaches -v 0
    But in some papers and tools I see that thay allowed 1 mistmache?! I compared the results in both way. Most of the counts are similar but for some miRNAs thay are doubled like in mir143 bellow:

    with 1 mistmach mapping:
    miR-143 - 4,697,060
    miR-10b - 520,833

    with 0 mistmach mapping:
    mir-143 - 1,976,574
    mir-10b - 501,099

    So which is the right way? I thought it should be with 0 mistmaches since non specific tags can align when mistmaches occure but some people do it? And if I want to estimate diff.expression I should know which method is most relevant?

    Thanks
    ------------
    SMART - bioinfo.uni-plovdiv.bg

  • #2
    vebaev,

    a straightforward way to check is to look at the alignments in any genomics viewer. It will tell you exactly which base(s) are not perfectly aligned for these genes. I believe some people allow one mismatch to accommodate sequencing errors or SNPs.

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