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  • qseq to fastq - post conversion quality trimming

    Hiya!

    I have a bunch of old RNAseq data sets that I want to re-analyse using our current pipeline. First challenge was that the data is old enough to have been archived in qseq format, not fastq. I converted all files using a neat little java tool found here:

    Free, secure and fast downloads from the largest Open Source applications and software directory - SourceForge.net


    Described here: http://www.biostars.org/p/6682/

    Has worked well and is pretty fast. My resulting fastq files, however, contain every single read - including the one with low quality and those that have a failed p/f flag. Therefore I want to some quality trimming before I move on to analysis.

    Does anyone have any tool recommendations? And, more importantly, a rational way of filtering? What would be a good quality cutoff to use? If I am not mistaken the quality scores spit out by the java tool are phred64.
    Cheers!

    TabeaK

  • #2
    qseq to fastq - post conversion quality trimming

    Trimmomatic is good for trimming Illumina data in fastq
    format.

    http://www.usadellab.org/cms/index.php?page=trimmomatic.

    Best wishes,
    Maria

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