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  • Need to reverse seq of read in Fastq2 (Illummia) for alignment

    Hi everyone!
    Present, I have two file *fastq (fastq_1 and fastq_2) of Illumina.
    follow me known: file fastq_1 is seq from 3' - 5', and fastq_2 is seq form 5' - 3'. So when I want to align between two file. Need to reverse reads of fastq_2? or the seq of fastq_2 was reversed automatically by Illumina?
    What should i do?
    Thanks for help.

  • #2
    They're both 5'->3' (nucleic acid sequences always are) and you don't need to reverse complement anything, just let the aligner deal with that.

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    • #3
      Ryan is right. As far as I know you only have to do this for mate-paired sequencing.

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      • #4
        Originally posted by lindenb View Post
        Ryan is right. As far as I know you only have to do this for mate-paired sequencing.
        Thanks to help. Yesterday, I sent an email to technical Illumina and they were reply same Dryan cmt.

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