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  • cufflink assemble result

    Hi everyone,

    I used tophat and cufflinks to assemble RNA-seq data. The result is good when the reads coverage is high. But I am confused the result when reads coverage is low. I attatched an example
    11.pdf
    why the exons identified by cufflinks is divided into 5 pieces ? I think they should conbimed into 2 exons according to the comparison of gene models, and it also seems ignore the junction information identified by tophat. Does anyone have some ideas
    Last edited by syslm01; 07-16-2010, 08:15 AM.

  • #2
    What version did you use?

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    • #3
      I used the TopHat v1.0.13 and cufflinks v0.8.2 version.
      Last edited by syslm01; 07-16-2010, 10:28 PM.

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