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The Per base sequence quality report does not look great, but more importantly, nearly 1.5% of all the sequences are all A's according to the Overrepresented sequences. This is something that often comes up in miseq data that has shorter insert sizes than the overall read length. Next we'll start looking at how to trim our data before continuing. |
FASTQ Processing Tools
FASTX Toolkit
The FASTX-Toolkit provides a set of command line tools for manipulating fasta and fastq files. The available modules are described on their website. They include a fast fastx_trimmer utility for trimming fastq sequences (and quality score strings) before alignment and fastx_clipper for trimming specific sequences (such as adapters).
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