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  • sowmyai
    Member
    • Jan 2010
    • 27

    #1

    Sequencing ssRNA virus using Bowtie

    I am trying to assemble reads from an ssRNA virus into a reference genome. In this case, does strand bias apply ? Also, how should the second column of the Bowtie output "Reference strand(+/-) of the reference genome" be interpreted ? Should I discard all the - rows and only keep rows that align to the + strand of the reference ? Maybe I don't understand RNA and cDNA biology enough. Could someone please explain ?
  • sowmyai
    Member
    • Jan 2010
    • 27

    #2
    One more question. Are Solexa paired-end read mates from the same or opposite strands ?

    Comment

    • Melissa
      Senior Member
      • Aug 2008
      • 124

      #3
      Both strands can be sequenced. So do not discard the - strand. Somebody in the forum should be able to explain this better.

      Comment

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