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  • TopHat and Cufflinks; closure search

    Dear All,
    Should cufflinks also include a closure-search option that is included with TopHat?

    tophat has;
    -r/--mate-inner-dist = distance between paired end reads
    --mate-std-dev = std deviation of this distance

    and an option to deal with overlapping reads from paired ends
    --closure-search

    Likewise cufflinks has;
    -m = distance between paired end reads
    -s = std deviation of this distance

    But there is no closure search in cufflinks. As I see overlapping reads in my data and I assume it has happened to other peoples datasets, should cufflinks also have a closure search like tophat?

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