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  • Tophat and cufflinks mate-inner-dist option

    I'd like to run two programs for the paired-end reads.
    The question is that if the mate-inner-dist is less than 0, can I put the number which is less that 0?

    For example, when the RNA fragment size in the library is around 140bp and the read length is 75bp, theoretically, mate-inner-dist is going to be "-10" (75*2-140).
    In this case, do I have to put the "-10" or simply "0"?

  • #2
    I had the same question before and it was answered by Cole Trapnell in this thread:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    basically you can specify a negative integer. My results tell me that they were correctly mapped.

    Originally posted by combiochem View Post
    I'd like to run two programs for the paired-end reads.
    The question is that if the mate-inner-dist is less than 0, can I put the number which is less that 0?

    For example, when the RNA fragment size in the library is around 140bp and the read length is 75bp, theoretically, mate-inner-dist is going to be "-10" (75*2-140).
    In this case, do I have to put the "-10" or simply "0"?

    Comment


    • #3
      Thanks for the comments and the the other post. It helps.

      Comment

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