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  • How to choose Tophat/Cufflinks Library Type for SOLiD data?

    Hi all,
    I have some unoriented data based on SOLiD 3 plus system, which Library Type should I choose when I running Tophat and Cufflinks?

    Thanks!

  • #2
    I presume you are specifying these as '--single' reads. If so then I would put '-SS_lib_type' as 'F'.

    Comment


    • #3
      yes, it is single reads, but I didn't find '--single' parameter in cufflinks and tophat?

      Comment


      • #4
        My mistake. I was thinking of a different program other than tophat. Library type should be '
        fr-secondstrand'

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