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  • Alignment PE reads with different length by TopHat

    Hello!
    I want to know if TopHat 1.2.0 can work with paired-end reads of different lenght without problems.
    Can I modify the -r/--mate-inner-dist for correct output?

    Example: I have sample with insert size of 200bp, the first read of 75bp and the second read of 50bp (for quality decrease).
    Can I modify -r option as 200-(75-50)? is correct?

    Are there other TopHat options that I must to consider?

    Thanks in advance

    Valeria

  • #2
    Welcome Valeria,

    as for your question, I'll give you the same answer I got when I asked my first question on this thread: go to the bioinformatics forum and ask there.

    That's where people will read it and answer it.

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