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  • should I reverse paired end reads before mapping?

    Hi , I am starting with tophat.

    I have a paired end illumina HISeq RNA Seq dataset with two files:

    SRR12331_1.fastq and SRR12331_2.fastq

    should I reverse the reads files in SRR_2.fastq before mapping with tophat?

    say I have a read from SRR12331_2.fastq:
    TTTTGGG

    should i feed tophat with :

    GGGTTTT

    THANKS!

  • #2
    nope leave them as they are the reads would have been generated as
    -----> <-------
    pairs which is the expected form by all aligners designed to deal with illumina paired-end data. The only time you may do this is with illumina mate-pair data which generates data
    <------ --------->

    Comment


    • #3
      You don't need to do reverse complement for the second set of read.
      As Jon_Keats said, most mainstream aligners are designed to deal with Illumina paired-end reads.
      I never used tophat, but I've used BWA, and it can map paired-end reads to ref seq perfectly.

      Comment

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