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Trim bases from both ends (Figure 4) allows user to keep only bases from a fixed start and end position of the reads. This is particularly useful if poor quality bases are observed on both ends  of the read. So instead of performing trim bases successively from the 5'- and 3'-end, the trim bases will only be performed once by trimming from both ends.

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].

Advanced options

In some cases, the reads that result from base trimming can have very short read lengths and thus are not recommended for alignment.Thus, Partek Flow provides the option to set a Min read length after base trimming. This discards reads that are shorter than the set length. 

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Figure 6 shows the options available for all the different selection of Trim bases function. Note the default Min read length is 25bp. For micro RNA sequencing data, this default Min read length needs to be set to a smaller value (we recommend 15) to account for mature microRNAs.

Trim Bases Task Details Page

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