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  • Newbler triming question

    Hello, I am using Newbler on cDNA transcriptome analysis. My input 454 sequences are trimmed ones. It seems that Newbler still trim them in a mysterious way which can't be found anywhere in the manual. Here are lines from 454NewblerMetrics.txt

    runData
    {
    file
    {
    path = "/xxx/xxx/xxx_trimmed.sff";

    numberOfReads = 771320, 715547;
    numberOfBases = 274290567, 273109839;
    }

    Is Newbler trimming my sequences according to quality?

    Thanks for your answers.

    Yu

  • #2
    Short answer: yes. Longer answer: probably, but I don't know the details. It is not possible to switch of this extra trimming.

    Comment


    • #3
      Actually in sff file, reads are not really trimmed, trimming points are labled. That's why we can use sffinfo -notrim to get the original reads. So input to GS software, they will find the trimming labels and use the the HQ parts of each reads.

      Comment


      • #4
        Originally posted by yuwang321 View Post
        Hello, I am using Newbler on cDNA transcriptome analysis. My input 454 sequences are trimmed ones. It seems that Newbler still trim them in a mysterious way which can't be found anywhere in the manual. Here are lines from 454NewblerMetrics.txt

        runData
        {
        file
        {
        path = "/xxx/xxx/xxx_trimmed.sff";

        numberOfReads = 771320, 715547;
        numberOfBases = 274290567, 273109839;
        }

        Is Newbler trimming my sequences according to quality?

        Thanks for your answers.

        Yu
        Newbler trims the reads such that the cleaned reads have average quality score of 20 or above and yokoyang mentioned above, it only labels the cut point and really not trim the bases out of read. I tried QTrim to trim the reads. (hiv.sanbi.ac.za/software/qtrim)

        Comment

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