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Trim bases from 5'-or 3'-end (Figures 2-3) allows a fixed number of bases to be trimmed away from the 5'- or 3'-end of the reads. These two functions are useful for when your read length is constant. This is not recommended if the read length is not constant, since good quality bases from shorter reads are likely trimmed away by these functions.

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Trim bases based on quality score (Figure 5) is probably the most useful function to trim poor quality bases from the 5'- or 3'-ends of reads. This function allows dynamic trimming of bases depending on quality score. The trimming can be done from either 5'-end, 3'-end or both ends of the reads. The function evaluates each base from the end of the read and trims it away until the last base has a quality score greater than the specified threshold. For an extensive evaluation of read trimming effects on Illumina NGS data analysis, see Del Fabbro et. al. [1]. 

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Trim Bases Task Details Page

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