Feb. 21, 2014, 5:41 p.m. by Rosalind Team
Topics: Bioinformatics Tools, NGS
Cannot milk it?
Once you detect the bad quality letters in your reads, a good strategy is not to filter out entire reads (as we do in “Read Filtration by Quality”) but trim low-quality bases from both ends of your reads. it helps to save a large amount of information.
Bad quality bases can be easily trimmed out using certain threshold (defined by quality plot similar to what we did in “Base Quality Distribution”) There is a lot of trimming tools, you can try one of following:
FASTQ Quality Trimmer tool on the Galaxy. It uses a "sliding window" approach so for a simple trimming of the ends you should set window size 1.
Trimmomatic. It is a command-line java-based tool, detail description and download link can be found here. For a simple trimming from both ends you should specify parameters LEADING and TRAILING.
Given: FASTQ file, quality cut-off value
Return: FASTQ file trimmed from the both ends (removed leading and trailing bases with quality lower than
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