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  • #1

    questions about metatranscriptom mapping to draft genome?

    we have sequenced metatranscriptome and metagenome by illumina hiseq2000.and we assembled 3 draft genome(bining sequences).I have mapped metatranscriptomic data to each of these drafts by soapaliner/soap2.
    This software can output two kinds of mapping results: PE--output file of paired alignment hits and SE--output file of unpaired alignment hits.the SE means upstream and downstream mates mapping to different contigs.
    My question is if I want to calculate the ration of metatranscriptomic data mapping to genomes,is there any problem that I discard the SE results and just use the PE results?Thanks!
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