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  • question about coverage, .ace file.

    Hi, I have benefited a lot form this forum, but I still have several questions while dealing with the 454 data.
    1), 454Alignment file indicates the depth of each position on the reference sequence, but it does not coincide with the .ace file, which I viewed under Eagle View, found coverage is not as described in the 454Alignment file.
    2), Really poor alignment found in the .ace file, especially at the ends of reads sometimes, many mismatches, why not the software shear them? and will these poor alignments be taken into account when produce the contig?
    3), Because the defect of homopolymer of 454, we plan to using solexa as a complement to help assembling, is it OK? and any reference available?

    Anyway, we are sequencing the MT DNA using 454, do you guys have any suggestion?

    Thanks.

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