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Archived Comments for: Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data

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  1. Incorrect description of Trimmomatic trimming function

    Ian John Donaldson, University of Manchester

    5 October 2015

    I would like to begin by saying this is an interesting study, however the description of Trimmomatic appears to be incorrect.  It is stated in the second paragraph of the results section that:

    "Adapter trimming increased the number of total reads in RNA-seq data, due to the fact that Trimmomatic had cut low quality bases from the middle portion of some of the reads, thus splitting some of them into multiple shorter reads, which still survived the minimum legth (10 bp) threshold ..."

    To my knowledge Trimmomatic 0.30 has no such functionality; the quality trimming method SLIDINGWINDOW cuts a read and removes the remainder when the mean quality value of a sliding window falls below a given value.



    Competing interests