Feb. 21, 2014, 5:41 p.m. by Rosalind Team
Topics: Bioinformatics Tools, NGS
Cannot milk it?
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
20 @Rosalind_0049 GCAGAGACCAGTAGATGTGTTTGCGGACGGTCGGGCTCCATGTGACACAG + FD@@;C<AI?4BA:=>C<G=:AE=><A??>764A8B797@A:58:527+, @Rosalind_0049 AATGGGGGGGGGAGACAAAATACGGCTAAGGCAGGGGTCCTTGATGTCAT + 1<<65:793967<4:92568-34:.>1;2752)24')*15;1,.3*3+*! @Rosalind_0049 ACCCCATACGGCGAGCGTCAGCATCTGATATCCTCTTTCAATCCTAGCTA + B:EI>JDB5=>DA?E6B@@CA?C;=;@@C:6D:3=@49;@87;::;;?8+
@Rosalind_0049 GCAGAGACCAGTAGATGTGTTTGCGGACGGTCGGGCTCCATGTGACAC + FD@@;C<AI?4BA:=>C<G=:AE=><A??>764A8B797@A:58:527 @Rosalind_0049 ATGGGGGGGGGAGACAAAATACGGCTAAGGCAGGGGTCCT + <<65:793967<4:92568-34:.>1;2752)24')*15; @Rosalind_0049 ACCCCATACGGCGAGCGTCAGCATCTGATATCCTCTTTCAATCCTAGCT + B:EI>JDB5=>DA?E6B@@CA?C;=;@@C:6D:3=@49;@87;::;;?8