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  • Running Newbler without trimming options

    Hi everyone,
    I have 4 transciptomes generated under the 454 platform. During the library prep there was some problems and Newbler can't remove the adaptors properly. Thus, I have trimmed adaptors and quality with a different software and now I would like to run Newbler using that input file (in fastaq format).

    The problem is that when I run the GUI version of Newbler 2.6, some reads are trimmed and I want to avoid that. The command line version offers the -notrim option but it seems that the input file in those cases have to be an sff file.

    Any suggestion? Can I use the -notrim command using a fastaq format input file?.

    Thanks a bunch.

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