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tophat, --mate-inner-dist and variable length reads

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  • tophat, --mate-inner-dist and variable length reads

    Hi there, I have variable length RNA-seq reads ranging from 42 to 76 bp (I guess because of a trimming process). Since I have to specify --mate-inner-dist parameter, which would be the correct value?
    Any hint is appreciated

    d

  • #2
    Originally posted by dawe View Post
    Hi there, I have variable length RNA-seq reads ranging from 42 to 76 bp (I guess because of a trimming process). Since I have to specify --mate-inner-dist parameter, which would be the correct value?
    Any hint is appreciated

    d
    I would suggest using some average value (mean, median, whatever) for --mate-inner-distance and accompanying that with an appropriate --mate-std-dev.

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    • #3
      Good point, thanks!
      Besides... I've realized I must know what trimming process has been applied. If 5' trimming, the inner size remains the same, if 3' trimming I will try to evaluate mean/stddev

      d

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