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  • sclindsay
    replied
    Hi Ben,

    If the coordinates reported are still correct, I'm assuming this means that if I feed a gff file to bowtie then the coordinates will still match?

    Thanks,

    Scott

    Leave a comment:


  • Ben Langmead
    replied
    Originally posted by ljxue View Post
    Does this mean that, by default, the total length of reference was shorten than the original sequence? In this case, does the site in the output file consist with the original sequences?
    The coordinate reported in the bowtie output will still be correct.

    Thanks,
    Ben

    Leave a comment:


  • ljxue
    started a topic Option for bowtie-build

    Option for bowtie-build

    Dear all,
    In the manual of bowtie:

    bowtie-build
    --ntoa Convert Ns in the reference sequence to As
    before building the index. By default, Ns
    are simply excluded from the index and
    'bowtie' will not find alignments that
    overlap them.



    Does this mean that, by default, the total length of reference was shorten than the original sequence? In this case, does the site in the output file consist with the original sequences?

    Thank you.

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