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  • #16
    What is your read-length distribution? The older versions of TopHat had problems, in case of too high length differences. Additionally, reads below 20 bp are very hard to map; I discard all reads below that length (denote you need to control for the pairing information).
    Otherwise, you can try a different aligner (e.g. STAR or bbmap).

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    • #17
      This was troublesome for me as well.

      Using the program bamtools helped no end ! Detailed in this post:



      It looks arcane but it's worked for me on thousands of samples. Hope that helps.

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