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Cuffcompare codes and use in novel non-coding gene discovery

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  • Cuffcompare codes and use in novel non-coding gene discovery

    Hi,

    I'm looking into lincRNA discovery and working through some cuffcompare output for a number of samples.

    I am curious whether people use these in discovery pipelines as hard filters ? I recognise a massive number are just classified as "Complete match of intron chain" but I'm unclear as to exactly what that means. From one set I get a massive number reported as such (roughly 99%). Are these normally considered as junk or is there just no reliable way to identify which of these are real ? I'm not sure if the fact that we're looking at a rRNA depleted set rather than polyA+ would affect this assumption?

    The numbers I got are below

    {'c': 251, 'e': 76, 'i': 528, 'j': 43, 'o': 28, '.': 306, 'p': 10, 's': 2, 'r': 45, 'x': 126, '=': 162089}

    Thanks,
    Warren
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